SMTL ID : 2afh.1

Crystal Structure of Nucleotide-Free Av2-Av1 Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.1: 7 residues within 4Å: Chain A: A.64, R.95, Q.190, G.423, I.424, H.441 Ligands: CFN.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.441 Hydrogen bonds: A:Q.190, A:I.424 Water bridges: A:G.94, A:K.425, A:K.425, A:K.425, A:K.425, B:R.104 Salt bridges: A:K.425, A:H.441, A:H.441 HCA.13: 8 residues within 4Å: Chain C: A.64, R.95, Q.190, G.423, I.424, K.425, H.441 Ligands: CFN.14 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.441 Hydrogen bonds: C:Q.190, C:I.424 Water bridges: C:G.94, C:R.96, C:K.425, C:K.425, C:K.425, C:K.425, C:E.439, D:Y.97, D:Y.97, D:R.104 Salt bridges: C:K.425, C:H.441, C:H.441

2 x CFN: FE(7)-MO-S(9)-N CLUSTER(Non-covalent)

CFN.2: 15 residues within 4Å: Chain A: V.69, R.95, H.194, Y.228, I.230, C.274, S.277, I.354, G.355, G.356, L.357, R.358, F.380, H.441 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.379 Metal complexes: A:C.274 CFN.14: 15 residues within 4Å: Chain C: V.69, R.95, H.194, Y.228, I.230, C.274, S.277, I.354, G.355, G.356, L.357, R.358, F.380, H.441 Ligands: HCA.13 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.379 Metal complexes: C:C.274

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 2 residues within 4Å: Chain A: D.203, W.204 No protein-ligand interaction detected (PLIP) PGE.4: 5 residues within 4Å: Chain A: T.302, I.305, E.306, W.334, D.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.306 Water bridges: A:R.309, A:R.309, A:D.368 PGE.9: 7 residues within 4Å: Chain B: P.294, W.295, E.298, K.314, L.315, N.316, R.400 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.298, B:K.314, B:R.400 Water bridges: B:N.316, B:N.316, B:N.316 PGE.17: 4 residues within 4Å: Chain C: L.466, N.467, W.471, K.472 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.467, C:K.472 PGE.19: 4 residues within 4Å: Chain C: T.302, I.305, W.334, D.368 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.368, C:D.368 Water bridges: C:E.306, C:R.342 PGE.21: 7 residues within 4Å: Chain D: P.294, W.295, E.298, K.314, L.315, N.316, R.400 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.314, D:L.315, D:R.400 Water bridges: D:N.316 PGE.22: 3 residues within 4Å: Chain D: E.32, K.33, Y.34 No protein-ligand interaction detected (PLIP) PGE.24: 3 residues within 4Å: Chain D: D.176, F.182, Y.206 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.176

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, D:R.107, D:E.108, H2O.14, H2O.51 CA.20: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:R.107, B:E.108, D:D.352, D:D.356, H2O.14, H2O.51

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.41

2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.7: 19 residues within 4Å: Chain A: C.61, Y.63, P.84, G.86, C.87, Y.90, E.152, C.153, G.184 Chain B: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.152 Metal complexes: A:C.61, A:C.87, A:C.87, A:C.153, B:C.69, B:C.94, B:C.94, B:C.152 CLF.15: 19 residues within 4Å: Chain C: C.61, Y.63, P.84, G.86, C.87, Y.90, E.152, C.153, G.184 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D, Salt bridges: C:E.152 Metal complexes: C:C.61, C:C.87, C:C.87, C:C.153, D:C.69, D:C.94, D:C.94, D:C.152

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 5 residues within 4Å: Chain B: M.212, K.215, V.217, W.308, K.309 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.212, B:V.217, B:W.308 TRS.16: 3 residues within 4Å: Chain C: E.286, P.292, W.293 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.293, C:W.293 Water bridges: C:E.286, C:E.295

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 6 residues within 4Å: Chain B: E.298, K.299, K.302, R.400 Chain F: E.110, Y.115 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:E.110, B:K.302 PG4.28: 5 residues within 4Å: Chain E: M.29, G.30, K.31, D.120, V.248 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.31, E:D.120

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.11: 9 residues within 4Å: Chain B: T.47, T.48, F.434, T.435, D.436, K.437, K.457, E.460, F.461 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.47, B:K.49, B:K.437 Water bridges: B:R.365, B:D.436 1PE.18: 8 residues within 4Å: Chain B: H.362, E.388, P.413, Y.414, K.416 Chain C: R.344, D.463, N.467 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.416, C:R.344 Water bridges: B:E.388, B:E.388, B:N.417, B:N.417, B:N.417

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 3 residues within 4Å: Chain B: Q.52, F.56, Y.421 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.421 Water bridges: B:Q.52 PEG.25: 2 residues within 4Å: Chain D: E.41, W.45 No protein-ligand interaction detected (PLIP) PEG.26: 7 residues within 4Å: Chain A: P.469 Chain D: K.380, L.383, E.384, S.412, P.413, Y.414 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.380, D:K.380, D:S.412

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.23: 7 residues within 4Å: Chain D: Q.52, F.56, K.402, T.419, V.420, Y.421, I.422 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.52, D:I.422, D:I.422

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.27: 10 residues within 4Å: Chain E: C.97, A.98, C.132, G.134, F.135 Chain F: C.97, A.98, G.99, C.132, G.134 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, Metal complexes: E:C.97, E:C.132, F:C.97, F:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tezcan, F.A. et al., Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein. Science (2005)

Release Date

2005-09-06

Peptides

Nitrogenase molybdenum-iron protein: AC
Nitrogenase molybdenum-iron protein: BD
Nitrogenase iron protein 1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Nitrogenase molybdenum-iron protein

Nitrogenase molybdenum-iron protein

Nitrogenase iron protein 1

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