Atomistry » Iron » PDB 3vsi-3wfd » 3vyt
Atomistry »
  Iron »
    PDB 3vsi-3wfd »
      3vyt »

Iron in PDB 3vyt: Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)

Protein crystallography data

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward), PDB code: 3vyt was solved by S.Watanabe, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.79 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.333, 99.412, 103.923, 90.00, 97.79, 90.00
R / Rfree (%) 20.7 / 25.3

Other elements in 3vyt:

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) (pdb code 3vyt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward), PDB code: 3vyt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3vyt

Go back to Iron Binding Sites List in 3vyt
Iron binding site 1 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:36.0
occ:1.00
FE1 B:SF4501 0.0 36.0 1.0
S2 B:SF4501 2.0 35.5 1.0
SG B:CYS323 2.3 34.5 1.0
S4 B:SF4501 2.3 33.4 1.0
S3 B:SF4501 2.3 36.7 1.0
FE2 B:SF4501 2.7 36.5 1.0
FE3 B:SF4501 2.9 38.1 1.0
FE4 B:SF4501 2.9 34.4 1.0
CB B:CYS323 3.5 38.9 1.0
CB B:CYS325 3.7 30.8 1.0
S1 B:SF4501 3.7 32.5 1.0
N B:CYS325 3.8 32.8 1.0
CA B:GLY352 3.8 32.5 1.0
CA B:CYS323 3.8 37.7 1.0
N B:ARG324 3.9 33.2 1.0
N B:GLY352 4.2 33.4 1.0
CA B:CYS325 4.2 32.2 1.0
C B:CYS323 4.3 43.7 1.0
C B:GLY352 4.7 25.2 1.0
C B:ARG324 4.7 38.8 1.0
SG B:CYS338 4.8 35.0 1.0
SG B:CYS345 4.9 39.1 1.0
SG B:CYS362 4.9 34.2 1.0
CA B:ARG324 4.9 40.3 1.0

Iron binding site 2 out of 4 in 3vyt

Go back to Iron Binding Sites List in 3vyt
Iron binding site 2 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:36.5
occ:1.00
FE2 B:SF4501 0.0 36.5 1.0
S4 B:SF4501 2.0 33.4 1.0
S3 B:SF4501 2.0 36.7 1.0
S1 B:SF4501 2.1 32.5 1.0
SG B:CYS345 2.3 39.1 1.0
FE1 B:SF4501 2.7 36.0 1.0
FE3 B:SF4501 2.8 38.1 1.0
FE4 B:SF4501 2.9 34.4 1.0
CB B:CYS345 3.3 41.3 1.0
S2 B:SF4501 3.8 35.5 1.0
N B:GLY352 3.9 33.4 1.0
CB B:MET355 4.0 28.8 1.0
CA B:GLY352 4.3 32.5 1.0
CB B:VAL351 4.5 35.6 1.0
CE B:MET355 4.6 19.9 1.0
N B:VAL351 4.7 37.7 1.0
SG B:CYS323 4.7 34.5 1.0
CA B:CYS345 4.7 36.5 1.0
CG B:MET355 4.8 26.6 1.0
C B:VAL351 4.8 33.3 1.0
SG B:CYS362 4.8 34.2 1.0
SG B:CYS338 4.9 35.0 1.0
CA B:VAL351 4.9 37.4 1.0
CB B:LEU340 4.9 35.9 1.0
O B:GLY352 5.0 36.0 1.0
CB B:CYS362 5.0 31.3 1.0

Iron binding site 3 out of 4 in 3vyt

Go back to Iron Binding Sites List in 3vyt
Iron binding site 3 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:38.1
occ:1.00
FE3 B:SF4501 0.0 38.1 1.0
SG B:CYS338 2.3 35.0 1.0
S1 B:SF4501 2.3 32.5 1.0
S2 B:SF4501 2.3 35.5 1.0
S4 B:SF4501 2.4 33.4 1.0
FE4 B:SF4501 2.8 34.4 1.0
FE2 B:SF4501 2.8 36.5 1.0
FE1 B:SF4501 2.9 36.0 1.0
CB B:CYS338 3.1 27.4 1.0
S3 B:SF4501 3.9 36.7 1.0
N B:ARG324 4.2 33.2 1.0
N B:PHE341 4.3 37.5 1.0
CB B:LEU340 4.4 35.9 1.0
CA B:CYS323 4.5 37.7 1.0
CA B:CYS338 4.5 36.3 1.0
SG B:CYS323 4.7 34.5 1.0
SG B:CYS362 4.7 34.2 1.0
CA B:PHE341 4.7 40.2 1.0
C B:LEU340 4.8 38.8 1.0
O B:PRO335 4.8 39.8 1.0
CB B:PHE341 4.9 36.9 1.0
SG B:CYS345 4.9 39.1 1.0
N B:LEU340 4.9 44.7 1.0
C B:CYS323 4.9 43.7 1.0
CA B:LEU340 4.9 36.8 1.0

Iron binding site 4 out of 4 in 3vyt

Go back to Iron Binding Sites List in 3vyt
Iron binding site 4 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:34.4
occ:1.00
FE4 B:SF4501 0.0 34.4 1.0
SG B:CYS362 2.2 34.2 1.0
S1 B:SF4501 2.2 32.5 1.0
S2 B:SF4501 2.3 35.5 1.0
S3 B:SF4501 2.5 36.7 1.0
FE3 B:SF4501 2.8 38.1 1.0
FE1 B:SF4501 2.9 36.0 1.0
FE2 B:SF4501 2.9 36.5 1.0
CB B:CYS362 3.2 31.3 1.0
S4 B:SF4501 3.9 33.4 1.0
CB B:CYS354 4.1 42.7 1.0
CA B:CYS362 4.6 39.6 1.0
CB B:PRO335 4.7 36.6 1.0
N B:MET355 4.8 39.1 1.0
CB B:CYS325 4.8 30.8 1.0
CG2 B:VAL328 4.8 31.4 1.0
SG B:CYS338 4.9 35.0 1.0
CB B:MET355 4.9 28.8 1.0
CA B:CYS325 4.9 32.2 1.0
CB B:CYS338 4.9 27.4 1.0
N B:CYS325 4.9 32.8 1.0
CA B:PRO335 5.0 30.0 1.0
SG B:CYS345 5.0 39.1 1.0

Reference:

S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Crystal Structures of the Hypcd Complex and the Hypcde Ternary Complex: Transient Intermediate Complexes During [Nife] Hydrogenase Maturation Structure V. 20 2124 2012.
ISSN: ISSN 0969-2126
PubMed: 23123111
DOI: 10.1016/J.STR.2012.09.018
Page generated: Sun Dec 13 15:25:27 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy