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Iron in PDB 2gyq: Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.

Protein crystallography data

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq was solved by J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.70 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.451, 101.125, 103.802, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.6

Other elements in 2gyq:

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. (pdb code 2gyq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 2gyq

Go back to Iron Binding Sites List in 2gyq
Iron binding site 1 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.1
occ:1.00
OE1 A:GLU114 2.0 9.5 0.5
OE1 A:GLU117 2.1 16.1 1.0
OE1 A:GLU147 2.1 22.1 1.0
NE2 A:HIS52 2.2 10.1 0.7
O A:HOH585 2.3 25.0 1.0
OE2 A:GLU114 2.3 17.1 0.5
O A:HOH534 2.3 18.1 1.0
OE1 A:GLU114 2.4 15.6 0.5
CD A:GLU114 2.7 14.2 0.5
CD A:GLU147 3.1 14.6 1.0
CD A:GLU114 3.1 8.3 0.5
CD A:GLU117 3.1 12.5 1.0
CD2 A:HIS52 3.2 15.5 0.7
CE1 A:HIS52 3.2 11.5 0.7
ZN A:ZN409 3.3 13.5 0.6
O A:HOH591 3.3 18.3 0.3
ZN A:ZN407 3.4 17.6 1.0
OE2 A:GLU147 3.4 13.8 1.0
OE2 A:GLU114 3.5 11.6 0.5
OE2 A:GLU117 3.5 16.1 1.0
O A:HOH459 3.8 25.6 1.0
CG A:GLU114 4.2 12.5 0.5
CG A:GLU147 4.3 13.8 1.0
ND1 A:HIS52 4.3 10.7 0.7
CG A:HIS52 4.3 16.5 0.7
CG A:GLU117 4.4 11.5 1.0
O A:HOH577 4.4 28.1 1.0
CG A:GLU114 4.5 9.7 0.5
CA A:GLU114 4.6 9.1 0.5
CB A:GLU147 4.6 12.5 1.0
CA A:GLU114 4.6 9.5 0.5
CA A:GLU147 4.7 13.5 1.0
OG1 A:THR56 4.8 15.3 1.0
O A:HOH572 4.8 27.9 1.0
CB A:GLU114 4.8 9.8 0.5
CB A:GLU117 4.8 8.9 1.0
CD1 A:ILE29 4.8 11.5 1.0
CB A:GLU114 4.8 10.3 0.5
OE1 A:GLN59 4.9 10.0 0.6
CG1 A:VAL113 4.9 11.1 1.0

Iron binding site 2 out of 5 in 2gyq

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Iron binding site 2 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:10.3
occ:1.00
OH A:TYR116 1.9 11.5 1.0
OD2 A:ASP21 2.1 10.6 1.0
OE2 B:GLU88 2.1 14.7 1.0
SG A:CYS79 2.3 11.7 1.0
OE1 B:GLU88 2.5 17.0 1.0
OD1 A:ASP21 2.6 12.2 1.0
CG A:ASP21 2.7 10.4 1.0
CD B:GLU88 2.7 14.3 1.0
CZ A:TYR116 3.1 10.3 1.0
CB A:CYS79 3.3 9.7 1.0
CE2 A:TYR116 3.6 11.4 1.0
CA A:CYS79 3.8 9.1 1.0
NE A:ARG120 4.1 12.4 1.0
CB A:ALA81 4.1 8.7 1.0
CB A:ASP21 4.2 9.3 1.0
NH2 A:ARG120 4.2 13.6 1.0
CG B:GLU88 4.2 11.8 1.0
CE1 A:TYR116 4.2 10.6 1.0
O B:HOH460 4.4 21.1 1.0
C A:CYS79 4.5 9.2 1.0
O A:HOH424 4.5 12.5 1.0
O A:HOH422 4.6 13.7 1.0
N A:ALA81 4.6 8.6 1.0
CZ A:ARG120 4.6 11.6 1.0
O A:ASP21 4.8 8.6 1.0
N A:PRO80 4.9 9.0 1.0
C A:ASP21 4.9 7.9 1.0
CA A:ALA81 4.9 8.3 1.0
N A:ILE82 4.9 7.5 1.0
CA A:ASP21 5.0 8.7 1.0

Iron binding site 3 out of 5 in 2gyq

Go back to Iron Binding Sites List in 2gyq
Iron binding site 3 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:14.4
occ:1.00
OE2 A:GLU88 1.5 6.6 0.6
OH B:TYR116 2.0 12.1 0.7
OD2 B:ASP21 2.1 12.8 1.0
SG B:CYS79 2.2 16.1 1.0
CD A:GLU88 2.4 10.6 0.6
OD1 B:ASP21 2.5 13.9 1.0
OE1 A:GLU88 2.6 14.4 0.6
CG B:ASP21 2.7 9.9 1.0
OE2 A:GLU88 3.1 13.6 0.4
OH B:TYR116 3.1 10.8 0.3
CZ B:TYR116 3.2 10.1 0.7
CB B:CYS79 3.2 10.6 1.0
CE2 B:TYR116 3.8 10.0 0.7
CA B:CYS79 3.8 10.0 1.0
CE1 B:TYR116 3.8 10.8 0.3
CZ B:TYR116 3.9 11.5 0.3
CG A:GLU88 4.0 10.8 0.6
NH2 B:ARG120 4.1 18.0 1.0
O B:HOH516 4.1 30.6 1.0
CD A:GLU88 4.1 11.9 0.4
NE B:ARG120 4.1 15.3 1.0
CB B:ASP21 4.2 10.1 1.0
CE1 B:TYR116 4.3 10.3 0.7
CB B:ALA81 4.3 11.6 1.0
CG A:GLU88 4.5 12.3 0.4
C B:CYS79 4.5 9.4 1.0
O A:HOH590 4.6 18.4 1.0
O B:HOH418 4.6 14.1 1.0
N B:ALA81 4.6 9.4 1.0
CZ B:ARG120 4.7 16.6 1.0
O B:ASP21 4.8 8.9 1.0
N B:PRO80 4.9 9.2 1.0
C B:ASP21 4.9 8.4 1.0
O1 B:EDO413 4.9 27.9 1.0
CA B:ASP21 5.0 8.0 1.0

Iron binding site 4 out of 5 in 2gyq

Go back to Iron Binding Sites List in 2gyq
Iron binding site 4 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe404

b:11.2
occ:1.00
OE2 B:GLU117 2.0 17.2 1.0
OE1 B:GLU147 2.0 12.2 1.0
OE1 B:GLN59 2.0 9.8 1.0
O B:HOH428 2.1 16.3 1.0
OE1 B:GLU26 2.1 9.3 1.0
OE2 B:GLU26 2.3 10.7 1.0
CD B:GLU26 2.5 11.8 1.0
CD B:GLU117 3.0 11.0 1.0
CD B:GLU147 3.0 9.1 1.0
CD B:GLN59 3.1 9.9 1.0
OE2 B:GLU147 3.2 10.8 1.0
OE1 B:GLU117 3.4 14.1 1.0
FE B:FE405 3.6 13.3 1.0
NE2 B:GLN59 3.6 11.2 1.0
O B:HOH567 3.6 25.9 1.0
CG B:GLU26 4.1 10.6 1.0
CG B:GLU117 4.2 9.2 1.0
OG1 B:THR56 4.3 13.6 1.0
CG B:GLU147 4.3 10.4 1.0
CG2 B:THR56 4.4 13.3 1.0
CG B:GLN59 4.4 10.2 1.0
CE2 B:TYR121 4.5 9.2 1.0
CB B:GLN59 4.6 9.0 1.0
OH B:TYR121 4.6 9.4 1.0
CD1 B:ILE29 4.6 14.3 1.0
CB B:GLU117 4.7 8.3 1.0
NE2 B:HIS52 4.7 10.9 1.0
CB B:THR56 4.8 11.6 1.0
CB B:GLU26 4.9 9.1 1.0
CA B:THR56 5.0 12.0 1.0

Iron binding site 5 out of 5 in 2gyq

Go back to Iron Binding Sites List in 2gyq
Iron binding site 5 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:13.3
occ:1.00
O B:HOH567 1.5 25.9 1.0
OE2 B:GLU147 2.0 10.8 1.0
OE1 B:GLU117 2.1 14.1 1.0
OE1 B:GLU114 2.1 15.2 1.0
NE2 B:HIS52 2.1 10.9 1.0
OE2 B:GLU114 2.4 19.1 1.0
O B:HOH428 2.5 16.3 1.0
CD B:GLU114 2.6 13.9 1.0
CD B:GLU147 2.9 9.1 1.0
CE1 B:HIS52 3.1 11.0 1.0
CD B:GLU117 3.1 11.0 1.0
CD2 B:HIS52 3.2 12.3 1.0
OE1 B:GLU147 3.4 12.2 1.0
OE2 B:GLU117 3.5 17.2 1.0
FE B:FE404 3.6 11.2 1.0
CG B:GLU147 4.0 10.4 1.0
CB B:GLU147 4.1 7.8 1.0
CG B:GLU114 4.1 12.2 1.0
CH3 B:ACT415 4.2 26.6 1.0
CA B:GLU147 4.2 7.8 1.0
ND1 B:HIS52 4.2 12.1 1.0
CG B:HIS52 4.3 11.0 1.0
CG B:GLU117 4.4 9.2 1.0
NE2 B:GLN59 4.6 11.2 1.0
OE1 B:GLN59 4.7 9.8 1.0
CA B:GLU114 4.7 10.0 1.0
OG1 B:THR56 4.7 13.6 1.0
CB B:GLU117 4.8 8.3 1.0
CB B:GLU114 4.8 10.5 1.0
O B:ACT415 4.9 24.0 1.0
CB B:ALA150 4.9 10.9 1.0
N B:GLU147 4.9 7.5 1.0
C B:ACT415 5.0 27.9 1.0

Reference:

J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak. X-Ray Crystal Structure of Ycfi Protein, A Putative Structural Protein From Rhodopseudomonas Palustris. To Be Published.
Page generated: Sun Dec 13 14:45:45 2020

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