Atomistry » Iron » PDB 1wa6-1x71 » 1wui
Atomistry »
  Iron »
    PDB 1wa6-1x71 »
      1wui »

Iron in PDB 1wui: Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Enzymatic activity of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

All present enzymatic activity of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;

Protein crystallography data

The structure of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wui was solved by H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.069, 125.966, 66.380, 90.00, 90.00, 90.00
R / Rfree (%) 9.8 / 13.4

Other elements in 1wui:

The structure of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1wui). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 1wui:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 1 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:6.6
occ:0.99
 FE1 S:SF41001 0.0 6.6 1.0
S4 S:SF41001 2.2 7.1 1.0
SG S:CYS17 2.3 6.9 1.0
S2 S:SF41001 2.3 6.9 1.0
S3 S:SF41001 2.3 7.1 1.0
FE2 S:SF41001 2.7 6.8 1.0
FE3 S:SF41001 2.7 6.7 1.0
FE4 S:SF41001 2.7 6.7 1.0
CB S:CYS17 3.3 7.4 1.0
N S:CYS17 3.8 7.3 1.0
S1 S:SF41001 3.9 7.1 1.0
CA S:CYS17 4.0 7.0 1.0
N S:GLY19 4.2 6.8 1.0
CE1 L:HIS235 4.2 4.8 1.0
CA S:GLY19 4.5 6.7 1.0
O S:HOH5627 4.5 7.4 1.0
C S:CYS17 4.5 6.9 1.0
N S:THR18 4.5 7.4 1.0
N S:CYS20 4.6 6.8 1.0
CG L:ARG79 4.7 6.6 1.0
SG S:CYS114 4.7 7.3 1.0
SG S:CYS150 4.7 6.7 1.0
SG S:CYS20 4.8 7.1 1.0
ND1 L:HIS235 4.8 8.2 1.0
C S:GLU16 4.9 6.8 1.0
C S:GLY19 5.0 6.3 1.0
O L:ARG79 5.0 7.0 1.0

Iron binding site 2 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 2 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:6.8
occ:0.99
 FE2 S:SF41001 0.0 6.8 1.0
S3 S:SF41001 2.3 7.1 1.0
SG S:CYS114 2.3 7.3 1.0
S4 S:SF41001 2.3 7.1 1.0
S1 S:SF41001 2.3 7.1 1.0
FE3 S:SF41001 2.7 6.7 1.0
FE1 S:SF41001 2.7 6.6 1.0
FE4 S:SF41001 2.7 6.7 1.0
CB S:CYS114 3.3 7.0 1.0
S2 S:SF41001 3.9 6.9 1.0
O S:HOH5045 4.0 8.1 1.0
O S:HOH5027 4.0 7.7 1.0
N S:CYS114 4.0 6.5 1.0
O S:HOH5627 4.1 7.4 1.0
CA S:CYS114 4.2 7.0 1.0
SG S:CYS150 4.5 6.7 1.0
SG S:CYS20 4.7 7.1 1.0
SG S:CYS17 4.8 6.9 1.0
N S:CYS17 4.9 7.3 1.0
CA S:GLU16 5.0 7.1 1.0

Iron binding site 3 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 3 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:6.7
occ:0.99
 FE3 S:SF41001 0.0 6.7 1.0
S2 S:SF41001 2.3 6.9 1.0
SG S:CYS150 2.3 6.7 1.0
S1 S:SF41001 2.3 7.1 1.0
S4 S:SF41001 2.3 7.1 1.0
FE2 S:SF41001 2.7 6.8 1.0
FE1 S:SF41001 2.7 6.6 1.0
FE4 S:SF41001 2.7 6.7 1.0
CB S:CYS150 3.4 6.8 1.0
CA S:CYS150 3.5 6.7 1.0
C S:CYS150 3.8 6.6 1.0
O S:HOH5045 3.9 8.1 1.0
S3 S:SF41001 3.9 7.1 1.0
CG L:ARG79 4.1 6.6 1.0
O S:CYS150 4.2 6.7 1.0
N S:PRO151 4.3 6.2 1.0
SG S:CYS114 4.4 7.3 1.0
ND1 L:HIS235 4.6 8.2 1.0
SG S:CYS17 4.6 6.9 1.0
CE1 L:HIS235 4.7 4.8 1.0
CA S:PRO151 4.7 6.4 1.0
NE L:ARG79 4.7 6.5 1.0
O S:GLY149 4.7 6.5 1.0
SG S:CYS20 4.7 7.1 1.0
N S:CYS150 4.8 6.3 1.0

Iron binding site 4 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 4 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:6.7
occ:0.99
 FE4 S:SF41001 0.0 6.7 1.0
SG S:CYS20 2.2 7.1 1.0
S1 S:SF41001 2.3 7.1 1.0
S2 S:SF41001 2.3 6.9 1.0
S3 S:SF41001 2.3 7.1 1.0
FE1 S:SF41001 2.7 6.6 1.0
FE2 S:SF41001 2.7 6.8 1.0
FE3 S:SF41001 2.7 6.7 1.0
CB S:CYS20 3.5 6.7 1.0
N S:CYS20 3.6 6.8 1.0
S4 S:SF41001 3.9 7.1 1.0
O S:HOH5027 3.9 7.7 1.0
CA S:CYS20 4.0 6.8 1.0
CA S:PRO151 4.4 6.4 1.0
CB S:PRO151 4.4 6.5 1.0
C S:GLY19 4.5 6.3 1.0
CA S:GLY112 4.5 6.9 1.0
SG S:CYS17 4.7 6.9 1.0
OE1 S:GLU75 4.7 8.5 1.0
O S:GLY149 4.8 6.5 1.0
CA S:CYS150 4.8 6.7 1.0
N S:PRO151 4.8 6.2 1.0
CA S:GLY19 4.8 6.7 1.0
SG S:CYS150 4.9 6.7 1.0
SG S:CYS114 4.9 7.3 1.0
N S:GLY19 4.9 6.8 1.0

Iron binding site 5 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 5 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:8.3
occ:0.99
 FE1 S:SF41002 0.0 8.3 1.0
ND1 S:HIS188 2.0 8.6 1.0
S3 S:SF41002 2.3 8.2 1.0
S4 S:SF41002 2.3 8.2 1.0
S2 S:SF41002 2.3 8.8 1.0
FE3 S:SF41002 2.7 8.0 1.0
FE4 S:SF41002 2.7 8.2 1.0
FE2 S:SF41002 2.7 7.7 1.0
CE1 S:HIS188 3.0 10.1 1.0
CG S:HIS188 3.1 8.4 1.0
CB S:HIS188 3.6 8.5 1.0
S1 S:SF41002 3.9 7.9 1.0
CA S:HIS188 3.9 7.9 1.0
NE2 S:HIS188 4.1 10.3 1.0
CD2 S:HIS188 4.2 9.6 1.0
CD S:PRO225 4.2 8.6 1.0
CG S:PRO225 4.3 9.7 1.0
CB S:CYS191 4.5 8.6 1.0
O S:HIS188 4.5 8.4 1.0
SG S:CYS191 4.6 8.1 1.0
SG S:CYS216 4.6 8.6 1.0
C S:HIS188 4.7 8.1 1.0
SG S:CYS222 4.7 7.6 1.0
CD2 S:PHE197 4.7 12.3 1.0
N S:PRO225 4.8 8.3 1.0
CA S:GLY224 5.0 7.7 1.0
N S:HIS188 5.0 7.7 1.0

Iron binding site 6 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 6 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:7.7
occ:1.00
 FE2 S:SF41002 0.0 7.7 1.0
S4 S:SF41002 2.3 8.2 1.0
SG S:CYS222 2.3 7.6 1.0
S3 S:SF41002 2.3 8.2 1.0
S1 S:SF41002 2.3 7.9 1.0
FE3 S:SF41002 2.7 8.0 1.0
FE1 S:SF41002 2.7 8.3 1.0
FE4 S:SF41002 2.8 8.2 1.0
CB S:CYS222 3.2 7.1 1.0
S2 S:SF41002 3.9 8.8 1.0
CG2 S:VAL243 4.3 8.6 1.0
N S:GLY224 4.5 7.4 1.0
CA S:CYS222 4.5 7.2 1.0
CA S:GLY224 4.6 7.7 1.0
CD S:PRO225 4.6 8.6 1.0
ND1 S:HIS188 4.6 8.6 1.0
SG S:CYS216 4.7 8.6 1.0
SG S:CYS191 4.7 8.1 1.0
C S:CYS222 4.8 7.0 1.0
CB S:LEU217 4.8 7.7 1.0
N S:LEU217 4.8 7.8 1.0
N S:TYR218 4.8 8.2 1.0
C S:LEU217 5.0 8.0 1.0
O S:CYS222 5.0 7.8 1.0

Iron binding site 7 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 7 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:8.0
occ:0.99
 FE3 S:SF41002 0.0 8.0 1.0
SG S:CYS191 2.3 8.1 1.0
S2 S:SF41002 2.3 8.8 1.0
S1 S:SF41002 2.3 7.9 1.0
S4 S:SF41002 2.3 8.2 1.0
FE1 S:SF41002 2.7 8.3 1.0
FE2 S:SF41002 2.7 7.7 1.0
FE4 S:SF41002 2.7 8.2 1.0
CB S:CYS191 3.1 8.6 1.0
S3 S:SF41002 3.9 8.2 1.0
CB S:ARG193 4.0 9.1 1.0
CG1 S:VAL243 4.3 9.0 1.0
ND1 S:HIS188 4.4 8.6 1.0
CA S:CYS191 4.5 8.1 1.0
CG2 S:VAL243 4.6 8.6 1.0
N S:ARG193 4.6 9.1 1.0
CA S:ARG193 4.6 9.5 1.0
C S:ARG193 4.6 9.1 1.0
CG S:ARG193 4.7 9.3 1.0
N S:LEU194 4.7 9.5 1.0
SG S:CYS222 4.8 7.6 1.0
SG S:CYS216 4.9 8.6 1.0
CD S:ARG193 4.9 8.7 1.0
CB S:VAL243 5.0 7.6 1.0
C S:CYS191 5.0 8.6 1.0

Iron binding site 8 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 8 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:8.2
occ:1.00
 FE4 S:SF41002 0.0 8.2 1.0
S2 S:SF41002 2.3 8.8 1.0
SG S:CYS216 2.3 8.6 1.0
S1 S:SF41002 2.3 7.9 1.0
S3 S:SF41002 2.3 8.2 1.0
FE1 S:SF41002 2.7 8.3 1.0
FE3 S:SF41002 2.7 8.0 1.0
FE2 S:SF41002 2.8 7.7 1.0
CB S:CYS216 3.4 8.8 1.0
N S:LEU217 3.8 7.8 1.0
CA S:CYS216 3.9 8.8 1.0
S4 S:SF41002 3.9 8.2 1.0
N S:TYR218 4.2 8.2 1.0
C S:CYS216 4.3 8.1 1.0
CB S:PHE197 4.4 10.6 1.0
ND1 S:HIS188 4.4 8.6 1.0
CD2 S:PHE197 4.5 12.3 1.0
CB S:ARG193 4.5 9.1 1.0
CB S:TYR218 4.6 9.2 1.0
CE1 S:HIS188 4.7 10.1 1.0
CA S:LEU217 4.8 8.2 1.0
O S:ARG193 4.8 10.1 1.0
C S:LEU217 4.8 8.0 1.0
CG S:PHE197 4.8 11.5 1.0
SG S:CYS222 4.9 7.6 1.0
SG S:CYS191 4.9 8.1 1.0
CA S:TYR218 4.9 8.1 1.0
CB S:CYS222 5.0 7.1 1.0
C S:ARG193 5.0 9.1 1.0

Iron binding site 9 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 9 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:7.0
occ:1.00
 FE1 S:F3S1003 0.0 7.0 1.0
S1 S:F3S1003 2.2 8.0 1.0
S2 S:F3S1003 2.3 7.3 1.0
S3 S:F3S1003 2.3 7.4 1.0
SG S:CYS249 2.3 7.1 1.0
FE4 S:F3S1003 2.7 6.8 1.0
FE3 S:F3S1003 2.7 7.2 1.0
CB S:CYS249 3.2 6.5 1.0
CA S:CYS249 3.7 6.7 1.0
S4 S:F3S1003 3.9 7.3 1.0
N S:ILE250 4.1 6.7 1.0
N S:GLY251 4.2 6.9 1.0
C S:CYS249 4.3 7.0 1.0
N S:CYS252 4.5 6.7 1.0
CG2 S:THR227 4.6 7.8 1.0
CG2 S:VAL187 4.7 8.8 1.0
SG S:CYS231 4.8 8.1 1.0
CA S:GLY251 4.8 7.0 1.0
SG S:CYS252 4.8 7.3 1.0
NE2 L:GLN237 4.8 7.6 1.0
N S:CYS249 5.0 6.8 1.0

Iron binding site 10 out of 12 in 1wui

Go back to Iron Binding Sites List in 1wui
Iron binding site 10 out of 12 in the Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Ultra-High Resolution Structure of the Ni-A State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:7.2
occ:0.97
 FE3 S:F3S1003 0.0 7.2 1.0
S1 S:F3S1003 2.2 8.0 1.0
S4 S:F3S1003 2.3 7.3 1.0
S3 S:F3S1003 2.3 7.4 1.0
SG S:CYS231 2.3 8.1 1.0
FE4 S:F3S1003 2.7 6.8 1.0
FE1 S:F3S1003 2.7 7.0 1.0
CB S:CYS231 3.3 7.7 1.0
OD1 S:ASN229 3.9 9.9 1.0
S2 S:F3S1003 3.9 7.3 1.0
CE2 S:PHE236 4.3 8.5 1.0
O S:HOH5037 4.4 8.4 1.0
CG S:ASN229 4.5 7.3 1.0
CZ S:PHE236 4.5 8.1 1.0
CB S:ASN229 4.6 7.4 1.0
CG2 S:VAL187 4.6 8.8 1.0
CA S:CYS231 4.7 7.9 1.0
SG S:CYS252 4.8 7.3 1.0
CD S:PRO242 4.8 7.5 1.0
SG S:CYS249 4.8 7.1 1.0
CG S:PRO242 4.8 7.5 1.0

Reference:

H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, Y.Higuchi. Activation Process of [Nife] Hydrogenase Elucidated By High-Resolution X-Ray Analyses: Conversion of the Ready to the Unready State Structure V. 13 1635 2005.
ISSN: ISSN 0969-2126
PubMed: 16271886
DOI: 10.1016/J.STR.2005.07.018
Page generated: Sat Aug 3 16:36:21 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy