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Iron in PDB 2z1d: Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis

Protein crystallography data

The structure of Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis, PDB code: 2z1d was solved by S.Watanabe, R.Matsumi, T.Arai, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.49 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.253, 118.384, 81.165, 90.00, 100.89, 90.00
R / Rfree (%) 17.9 / 21.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis (pdb code 2z1d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis, PDB code: 2z1d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2z1d

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Iron binding site 1 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


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 [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.0
occ:1.00
 FE1 A:SF4501 0.0 25.0 1.0
SG A:CYS362 2.3 24.7 1.0
S3 A:SF4501 2.3 27.0 1.0
S2 A:SF4501 2.3 25.0 1.0
S4 A:SF4501 2.3 26.7 1.0
FE2 A:SF4501 2.7 24.9 1.0
FE3 A:SF4501 2.8 25.9 1.0
FE4 A:SF4501 2.8 25.9 1.0
CB A:CYS362 3.2 23.0 1.0
CB A:CYS354 3.7 27.2 0.5
S1 A:SF4501 3.8 26.0 1.0
SG A:CYS325 4.3 30.7 0.5
CB A:CYS354 4.5 26.4 0.5
SG A:CYS354 4.7 20.9 0.5
CA A:CYS362 4.7 21.9 1.0
N A:MET355 4.7 23.2 0.5
C A:CYS354 4.8 24.6 0.5
CA A:CYS354 4.8 24.5 0.5
SG A:CYS345 4.8 25.2 1.0
SG A:CYS338 4.9 25.2 1.0
N A:MET355 4.9 23.3 0.5
CB A:CYS338 4.9 24.0 1.0
CB A:MET355 4.9 24.5 0.5
CB A:MET355 4.9 23.8 0.5
CB A:PRO335 5.0 26.9 1.0

Iron binding site 2 out of 8 in 2z1d

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Iron binding site 2 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


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 [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:24.9
occ:1.00
 FE2 A:SF4501 0.0 24.9 1.0
S4 A:SF4501 2.2 26.7 1.0
S3 A:SF4501 2.2 27.0 1.0
S1 A:SF4501 2.2 26.0 1.0
SG A:CYS338 2.3 25.2 1.0
FE1 A:SF4501 2.7 25.0 1.0
FE3 A:SF4501 2.8 25.9 1.0
FE4 A:SF4501 2.8 25.9 1.0
CB A:CYS338 3.2 24.0 1.0
S2 A:SF4501 3.9 25.0 1.0
N A:ARG324 4.1 23.8 1.0
N A:PHE341 4.4 27.2 1.0
CB A:LEU340 4.4 27.9 1.0
CA A:CYS323 4.5 25.4 1.0
CA A:CYS338 4.6 30.8 1.0
SG A:CYS323 4.7 24.9 1.0
SG A:CYS362 4.7 24.7 1.0
CA A:PHE341 4.8 30.6 1.0
C A:LEU340 4.8 28.3 1.0
C A:CYS323 4.9 25.1 1.0
SG A:CYS345 4.9 25.2 1.0
N A:LEU340 4.9 31.6 1.0
CB A:CYS345 4.9 31.3 1.0
CB A:PHE341 4.9 29.6 1.0
CA A:LEU340 5.0 29.0 1.0

Iron binding site 3 out of 8 in 2z1d

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Iron binding site 3 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


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 [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.9
occ:1.00
 FE3 A:SF4501 0.0 25.9 1.0
S1 A:SF4501 2.3 26.0 1.0
S2 A:SF4501 2.3 25.0 1.0
SG A:CYS323 2.3 24.9 1.0
S4 A:SF4501 2.3 26.7 1.0
FE4 A:SF4501 2.7 25.9 1.0
FE2 A:SF4501 2.8 24.9 1.0
FE1 A:SF4501 2.8 25.0 1.0
SG A:CYS325 3.4 30.7 0.5
CB A:CYS323 3.5 24.6 1.0
CA A:CYS323 3.8 25.4 1.0
N A:CYS325 3.8 25.8 0.5
CB A:CYS325 3.8 23.0 0.5
N A:CYS325 3.8 26.6 0.5
N A:ARG324 3.9 23.8 1.0
S3 A:SF4501 3.9 27.0 1.0
CA A:GLY352 3.9 21.4 1.0
CB A:CYS325 4.0 27.7 0.5
C A:CYS323 4.2 25.1 1.0
N A:GLY352 4.2 23.5 1.0
CA A:CYS325 4.2 26.1 0.5
CA A:CYS325 4.3 27.3 0.5
CB A:CYS354 4.5 27.2 0.5
C A:ARG324 4.7 28.7 1.0
C A:GLY352 4.7 24.7 1.0
SG A:CYS338 4.8 25.2 1.0
SG A:CYS345 4.9 25.2 1.0
SG A:CYS362 4.9 24.7 1.0
CA A:ARG324 4.9 24.1 1.0
SG A:CYS325 4.9 25.6 0.5

Iron binding site 4 out of 8 in 2z1d

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Iron binding site 4 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


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 [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.9
occ:1.00
 FE4 A:SF4501 0.0 25.9 1.0
S1 A:SF4501 2.2 26.0 1.0
SG A:CYS345 2.3 25.2 1.0
S2 A:SF4501 2.3 25.0 1.0
S3 A:SF4501 2.3 27.0 1.0
FE3 A:SF4501 2.7 25.9 1.0
FE1 A:SF4501 2.8 25.0 1.0
FE2 A:SF4501 2.8 24.9 1.0
CB A:CYS345 3.2 31.3 1.0
S4 A:SF4501 3.9 26.7 1.0
N A:GLY352 3.9 23.5 1.0
CB A:MET355 4.2 23.8 0.5
CB A:MET355 4.2 24.5 0.5
CA A:GLY352 4.5 21.4 1.0
CB A:VAL351 4.5 29.4 1.0
CA A:CYS345 4.6 32.4 1.0
CE A:MET355 4.7 30.1 0.5
N A:VAL351 4.7 28.2 1.0
CE A:MET355 4.7 30.4 0.5
SG A:CYS323 4.8 24.9 1.0
SG A:CYS362 4.8 24.7 1.0
CG A:MET355 4.9 24.7 0.5
O A:GLY352 4.9 21.8 1.0
C A:VAL351 4.9 24.8 1.0
SG A:CYS338 4.9 25.2 1.0
CB A:CYS362 5.0 23.0 1.0
N A:MET355 5.0 23.2 0.5
CA A:VAL351 5.0 26.4 1.0

Iron binding site 5 out of 8 in 2z1d

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Iron binding site 5 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:26.8
occ:1.00
 FE1 B:SF4502 0.0 26.8 1.0
S2 B:SF4502 2.2 26.8 1.0
S4 B:SF4502 2.3 25.5 1.0
S3 B:SF4502 2.4 27.2 1.0
SG B:CYS323 2.4 26.1 1.0
FE2 B:SF4502 2.7 24.9 1.0
FE3 B:SF4502 2.8 25.7 1.0
FE4 B:SF4502 2.8 25.6 1.0
SG B:CYS325 3.2 24.3 0.4
CB B:CYS323 3.4 23.8 1.0
CA B:CYS323 3.8 23.2 1.0
N B:CYS325 3.8 25.4 0.6
N B:CYS325 3.8 24.9 0.4
N B:ARG324 3.9 22.3 1.0
S1 B:SF4502 3.9 26.9 1.0
CB B:CYS325 3.9 22.5 0.6
CA B:GLY352 4.0 25.2 1.0
CB B:CYS325 4.1 23.1 0.4
C B:CYS323 4.2 21.2 1.0
N B:GLY352 4.2 26.0 1.0
CA B:CYS325 4.3 27.3 0.6
CA B:CYS325 4.3 25.8 0.4
CB B:CYS354 4.6 27.8 0.6
C B:ARG324 4.6 26.6 1.0
SG B:CYS338 4.7 25.4 1.0
C B:GLY352 4.8 24.9 1.0
SG B:CYS345 4.8 24.1 1.0
CA B:ARG324 4.8 24.3 1.0
SG B:CYS362 4.9 24.7 1.0

Iron binding site 6 out of 8 in 2z1d

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Iron binding site 6 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:24.9
occ:1.00
 FE2 B:SF4502 0.0 24.9 1.0
S3 B:SF4502 2.2 27.2 1.0
S4 B:SF4502 2.2 25.5 1.0
S1 B:SF4502 2.3 26.9 1.0
SG B:CYS338 2.3 25.4 1.0
FE1 B:SF4502 2.7 26.8 1.0
FE3 B:SF4502 2.8 25.7 1.0
FE4 B:SF4502 2.8 25.6 1.0
CB B:CYS338 3.2 24.1 1.0
S2 B:SF4502 3.9 26.8 1.0
N B:ARG324 4.1 22.3 1.0
N B:PHE341 4.3 27.5 1.0
CB B:LEU340 4.3 29.1 1.0
CA B:CYS323 4.6 23.2 1.0
CA B:CYS338 4.6 25.3 1.0
SG B:CYS323 4.7 26.1 1.0
CA B:PHE341 4.7 25.5 1.0
SG B:CYS345 4.7 24.1 1.0
CB B:PHE341 4.8 24.3 1.0
SG B:CYS362 4.8 24.7 1.0
C B:LEU340 4.8 28.0 1.0
CB B:CYS345 4.8 23.7 1.0
CB B:ARG324 4.9 26.8 1.0
C B:CYS323 4.9 21.2 1.0
CG B:LEU340 4.9 32.9 1.0
CA B:LEU340 5.0 27.3 1.0
N B:LEU340 5.0 29.3 1.0
CA B:ARG324 5.0 24.3 1.0

Iron binding site 7 out of 8 in 2z1d

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Iron binding site 7 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:25.7
occ:1.00
 FE3 B:SF4502 0.0 25.7 1.0
SG B:CYS345 2.2 24.1 1.0
S2 B:SF4502 2.3 26.8 1.0
S4 B:SF4502 2.3 25.5 1.0
S1 B:SF4502 2.3 26.9 1.0
FE4 B:SF4502 2.7 25.6 1.0
FE1 B:SF4502 2.8 26.8 1.0
FE2 B:SF4502 2.8 24.9 1.0
CB B:CYS345 3.2 23.7 1.0
S3 B:SF4502 3.9 27.2 1.0
CB B:MET355 4.0 23.0 0.4
N B:GLY352 4.1 26.0 1.0
CB B:MET355 4.2 24.0 0.6
CE B:MET355 4.6 22.9 0.6
CB B:VAL351 4.6 29.7 1.0
CA B:GLY352 4.6 25.2 1.0
CA B:CYS345 4.6 27.5 1.0
CE B:MET355 4.7 23.1 0.4
N B:VAL351 4.7 26.2 1.0
CG B:MET355 4.8 19.5 0.4
SG B:CYS362 4.8 24.7 1.0
SG B:CYS323 4.9 26.1 1.0
SG B:CYS338 4.9 25.4 1.0
N B:MET355 4.9 22.7 0.6
CB B:CYS362 4.9 18.8 1.0
O B:GLY352 5.0 23.6 1.0

Iron binding site 8 out of 8 in 2z1d

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Iron binding site 8 out of 8 in the Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of [Nife] Hydrogenase Maturation Protein, Hypd From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:25.6
occ:1.00
 FE4 B:SF4502 0.0 25.6 1.0
S1 B:SF4502 2.2 26.9 1.0
SG B:CYS362 2.3 24.7 1.0
S3 B:SF4502 2.3 27.2 1.0
S2 B:SF4502 2.3 26.8 1.0
FE3 B:SF4502 2.7 25.7 1.0
FE2 B:SF4502 2.8 24.9 1.0
FE1 B:SF4502 2.8 26.8 1.0
CB B:CYS362 3.2 18.8 1.0
CB B:CYS354 3.6 27.8 0.6
S4 B:SF4502 3.9 25.5 1.0
SG B:CYS325 4.1 24.3 0.4
CB B:CYS354 4.5 18.9 0.4
SG B:CYS354 4.6 26.0 0.6
N B:MET355 4.7 22.7 0.6
CA B:CYS362 4.7 20.1 1.0
SG B:CYS345 4.7 24.1 1.0
CA B:CYS354 4.7 28.0 0.6
C B:CYS354 4.8 26.6 0.6
N B:MET355 4.9 21.5 0.4
SG B:CYS338 4.9 25.4 1.0
CB B:MET355 4.9 23.0 0.4
CB B:CYS338 5.0 24.1 1.0
CB B:PRO335 5.0 24.2 1.0
CB B:MET355 5.0 24.0 0.6

Reference:

S.Watanabe, R.Matsumi, T.Arai, H.Atomi, T.Imanaka, K.Miki. Crystal Structures of [Nife] Hydrogenase Maturation Proteins Hypc, Hypd, and Hype: Insights Into Cyanation Reaction By Thiol Redox Signaling Mol.Cell V. 27 29 2007.
ISSN: ISSN 1097-2765
PubMed: 17612488
DOI: 10.1016/J.MOLCEL.2007.05.039
Page generated: Sun Aug 4 05:49:29 2024

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