Atomistry » Iron » PDB 3vtj-3wg7 » 3vyr
Atomistry »
  Iron »
    PDB 3vtj-3wg7 »
      3vyr »

Iron in PDB 3vyr: Crystal Structure of the Hypc-Hypd Complex

Protein crystallography data

The structure of Crystal Structure of the Hypc-Hypd Complex, PDB code: 3vyr 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) 45.30 / 2.55
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.179, 181.179, 49.433, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Hypc-Hypd Complex (pdb code 3vyr). 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 Complex, PDB code: 3vyr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3vyr

Go back to Iron Binding Sites List in 3vyr
Iron binding site 1 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:48.6
occ:1.00
FE1 B:SF4501 0.0 48.6 1.0
SG B:CYS362 2.3 51.3 1.0
S4 B:SF4501 2.3 46.5 1.0
S3 B:SF4501 2.3 50.0 1.0
S2 B:SF4501 2.4 48.4 1.0
FE2 B:SF4501 2.7 49.3 1.0
FE4 B:SF4501 2.8 55.4 1.0
FE3 B:SF4501 2.9 49.5 1.0
CB B:CYS362 3.3 46.5 1.0
S1 B:SF4501 3.8 51.5 1.0
CB B:CYS354 4.2 42.0 1.0
CA B:CYS362 4.7 42.5 1.0
SG B:CYS338 4.8 56.0 1.0
SG B:CYS345 4.8 53.0 1.0
CG2 B:VAL328 4.8 35.0 1.0
CB B:PRO335 4.9 36.3 1.0
N B:CYS325 4.9 41.7 1.0
CB B:CYS325 4.9 32.0 1.0
CA B:CYS325 4.9 53.6 1.0
CE B:MET355 4.9 29.0 1.0
CB B:CYS338 4.9 54.0 1.0

Iron binding site 2 out of 4 in 3vyr

Go back to Iron Binding Sites List in 3vyr
Iron binding site 2 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:49.3
occ:1.00
FE2 B:SF4501 0.0 49.3 1.0
SG B:CYS338 2.3 56.0 1.0
S3 B:SF4501 2.3 50.0 1.0
S4 B:SF4501 2.3 46.5 1.0
S1 B:SF4501 2.4 51.5 1.0
FE1 B:SF4501 2.7 48.6 1.0
FE4 B:SF4501 2.8 55.4 1.0
FE3 B:SF4501 2.9 49.5 1.0
CB B:CYS338 3.2 54.0 1.0
S2 B:SF4501 3.8 48.4 1.0
N B:ARG324 4.1 42.6 1.0
N B:PHE341 4.3 57.7 1.0
CB B:LEU340 4.4 37.3 1.0
CA B:CYS323 4.6 52.5 1.0
CA B:CYS338 4.6 52.5 1.0
CB B:PHE341 4.7 51.1 1.0
CA B:PHE341 4.7 53.0 1.0
SG B:CYS323 4.8 48.7 1.0
SG B:CYS362 4.8 51.3 1.0
C B:LEU340 4.8 54.0 1.0
SG B:CYS345 4.9 53.0 1.0
C B:CYS323 4.9 51.5 1.0
CB B:ARG324 4.9 44.3 1.0
CB B:CYS345 5.0 61.6 1.0
CA B:LEU340 5.0 54.4 1.0
N B:LEU340 5.0 48.3 1.0

Iron binding site 3 out of 4 in 3vyr

Go back to Iron Binding Sites List in 3vyr
Iron binding site 3 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:49.5
occ:1.00
FE3 B:SF4501 0.0 49.5 1.0
S4 B:SF4501 2.1 46.5 1.0
SG B:CYS323 2.3 48.7 1.0
S1 B:SF4501 2.3 51.5 1.0
S2 B:SF4501 2.3 48.4 1.0
FE4 B:SF4501 2.7 55.4 1.0
FE2 B:SF4501 2.9 49.3 1.0
FE1 B:SF4501 2.9 48.6 1.0
CB B:CYS323 3.4 57.4 1.0
CA B:CYS323 3.7 52.5 1.0
N B:CYS325 3.7 41.7 1.0
CB B:CYS325 3.7 32.0 1.0
N B:ARG324 3.8 42.6 1.0
S3 B:SF4501 3.8 50.0 1.0
C B:CYS323 4.1 51.5 1.0
CA B:GLY352 4.1 38.1 1.0
CA B:CYS325 4.2 53.6 1.0
N B:GLY352 4.2 43.6 1.0
C B:ARG324 4.6 59.2 1.0
CA B:ARG324 4.8 50.0 1.0
SG B:CYS338 4.8 56.0 1.0
SG B:CYS345 4.8 53.0 1.0
SG B:CYS362 4.9 51.3 1.0
C B:GLY352 4.9 43.7 1.0

Iron binding site 4 out of 4 in 3vyr

Go back to Iron Binding Sites List in 3vyr
Iron binding site 4 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:55.4
occ:1.00
FE4 B:SF4501 0.0 55.4 1.0
S1 B:SF4501 1.9 51.5 1.0
S2 B:SF4501 1.9 48.4 1.0
S3 B:SF4501 2.0 50.0 1.0
SG B:CYS345 2.3 53.0 1.0
FE3 B:SF4501 2.7 49.5 1.0
FE2 B:SF4501 2.8 49.3 1.0
FE1 B:SF4501 2.8 48.6 1.0
CB B:CYS345 3.2 61.6 1.0
S4 B:SF4501 3.7 46.5 1.0
N B:GLY352 4.0 43.6 1.0
CB B:MET355 4.3 41.2 1.0
CB B:VAL351 4.4 46.0 1.0
CE B:MET355 4.5 29.0 1.0
CA B:GLY352 4.7 38.1 1.0
SG B:CYS323 4.7 48.7 1.0
CA B:CYS345 4.7 59.8 1.0
N B:VAL351 4.7 48.8 1.0
SG B:CYS362 4.7 51.3 1.0
SG B:CYS338 4.9 56.0 1.0
CA B:VAL351 4.9 39.4 1.0
C B:VAL351 4.9 48.3 1.0
CG B:MET355 5.0 36.5 1.0
CB B:CYS362 5.0 46.5 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 15:25:26 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy