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Zinc 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:

Iron (Fe) 5 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2gyq

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Zinc binding site 1 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn407

b:17.6
occ:1.00
OE2 A:GLU117 2.0 16.1 1.0
O A:HOH534 2.0 18.1 1.0
OE1 A:GLU26 2.0 11.8 1.0
OE2 A:GLU147 2.0 13.8 1.0
OE1 A:GLN59 2.3 10.0 0.6
OE2 A:GLU26 2.4 13.1 1.0
CD A:GLU26 2.5 11.3 1.0
CD A:GLU117 2.9 12.5 1.0
CD A:GLU147 3.0 14.6 1.0
OE1 A:GLU117 3.3 16.1 1.0
OE1 A:GLU147 3.3 22.1 1.0
CD A:GLN59 3.4 11.7 0.6
FE A:FE401 3.4 17.1 1.0
OE1 A:GLN59 3.7 16.1 0.4
NE2 A:GLN59 3.9 16.0 0.6
CG A:GLN59 4.0 13.4 0.4
CG A:GLU26 4.0 10.6 1.0
O A:HOH591 4.2 18.3 0.3
CG A:GLU117 4.2 11.5 1.0
OG1 A:THR56 4.3 15.3 1.0
CD A:GLN59 4.3 15.7 0.4
CD1 A:ILE29 4.3 11.5 1.0
CG A:GLU147 4.4 13.8 1.0
CG2 A:THR56 4.5 14.7 1.0
CB A:GLN59 4.6 12.2 0.4
CE2 A:TYR121 4.6 10.0 1.0
NE2 A:HIS52 4.6 10.1 0.7
CG A:GLN59 4.6 11.3 0.6
CB A:GLU117 4.7 8.9 1.0
OH A:TYR121 4.7 10.3 1.0
O A:HOH585 4.8 25.0 1.0
CB A:GLN59 4.8 12.2 0.6
CB A:THR56 4.8 13.6 1.0
CB A:GLU26 4.9 9.1 1.0
CA A:THR56 4.9 14.0 1.0

Zinc binding site 2 out of 6 in 2gyq

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Zinc binding site 2 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn409

b:13.5
occ:0.55
CD2 A:HIS52 1.5 15.5 0.7
OE2 A:GLU114 1.9 11.6 0.5
ND1 A:HIS52 2.0 8.4 0.3
O A:HOH459 2.1 25.6 1.0
NE2 A:HIS52 2.1 10.1 0.7
OE2 A:GLU114 2.4 17.1 0.5
CG A:HIS52 2.4 16.5 0.7
CD A:GLU114 2.8 8.3 0.5
O A:HOH585 2.9 25.0 1.0
CE1 A:HIS52 2.9 7.3 0.3
CD A:GLU114 3.0 14.2 0.5
CE1 A:HIS52 3.1 11.5 0.7
OE1 A:GLU114 3.1 9.5 0.5
CG A:HIS52 3.1 8.9 0.3
ND1 A:HIS52 3.2 10.7 0.7
O A:HOH577 3.2 28.1 1.0
FE A:FE401 3.3 17.1 1.0
CB A:HIS52 3.3 16.8 0.7
OE1 A:GLU114 3.4 15.6 0.5
CB A:HIS52 3.5 12.1 0.3
CB A:ALA150 3.7 16.4 1.0
CG A:GLU114 4.0 12.5 0.5
O A:HOH591 4.1 18.3 0.3
O A:HOH572 4.1 27.9 1.0
NE2 A:HIS52 4.1 8.7 0.3
CD2 A:HIS52 4.2 9.2 0.3
CG A:GLU114 4.2 9.7 0.5
O A:HOH503 4.5 46.8 0.7
O A:HOH534 4.5 18.1 1.0
CA A:HIS52 4.6 13.9 0.3
OE1 A:GLU147 4.7 22.1 1.0
CA A:HIS52 4.7 15.8 0.7

Zinc binding site 3 out of 6 in 2gyq

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Zinc binding site 3 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn410

b:14.1
occ:0.50
ZN A:ZN418 1.8 20.4 0.4
OE2 A:GLU95 1.9 20.8 1.0
NE2 B:HIS17 1.9 18.9 1.0
O A:HOH568 2.2 29.4 1.0
CD A:GLU95 2.7 16.2 1.0
CE1 B:HIS17 2.7 19.4 1.0
OE1 A:GLU95 2.8 24.7 1.0
O A:HOH419 2.9 9.0 1.0
CD2 B:HIS17 3.1 17.6 1.0
OE2 A:GLU91 3.7 21.5 0.5
O A:HOH554 3.8 40.6 1.0
ND1 B:HIS17 3.9 18.2 1.0
O A:HOH590 4.0 18.4 1.0
O A:HOH475 4.0 22.0 1.0
CG B:HIS17 4.1 13.7 1.0
CG A:GLU95 4.1 15.8 1.0
OG1 A:THR92 4.2 15.9 1.0
OE2 A:GLU91 4.2 16.1 0.5
CG A:GLU91 4.3 15.6 0.5
CD A:GLU91 4.5 17.8 0.5
CA A:THR92 4.6 12.1 1.0
OE1 A:GLU88 4.7 16.3 0.4
CG1 B:VAL77 4.7 13.0 0.4
CG2 B:VAL77 4.7 14.1 0.4
CG A:GLU91 4.8 12.1 0.5
CD A:GLU91 4.9 14.5 0.5
CB A:GLU95 4.9 13.6 1.0
N A:THR92 4.9 12.1 1.0
CB A:THR92 4.9 12.3 1.0

Zinc binding site 4 out of 6 in 2gyq

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Zinc binding site 4 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn418

b:20.4
occ:0.40
ZN A:ZN410 1.8 14.1 0.5
OE1 A:GLU95 1.8 24.7 1.0
O A:HOH568 1.8 29.4 1.0
O A:HOH554 2.0 40.6 1.0
CD A:GLU95 2.4 16.2 1.0
OE2 A:GLU95 2.5 20.8 1.0
NE2 B:HIS17 2.6 18.9 1.0
CD2 B:HIS17 3.0 17.6 1.0
CE1 B:HIS17 3.8 19.4 1.0
CG A:GLU95 3.9 15.8 1.0
CG2 B:VAL77 4.1 14.1 0.4
CG B:HIS17 4.4 13.7 1.0
O A:HOH475 4.4 22.0 1.0
O A:HOH419 4.5 9.0 1.0
OE2 A:GLU91 4.7 21.5 0.5
ND1 B:HIS17 4.7 18.2 1.0
CB A:GLU95 4.8 13.6 1.0
CG1 B:VAL77 4.8 13.0 0.4
CG1 B:VAL77 4.9 13.7 0.6
CB B:VAL77 5.0 13.0 0.6

Zinc binding site 5 out of 6 in 2gyq

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Zinc binding site 5 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn406

b:15.9
occ:0.85
O B:HOH434 2.0 19.3 1.0
OE1 B:GLU95 2.0 9.4 0.5
NE2 A:HIS17 2.0 12.2 1.0
OE1 B:GLU95 2.0 19.1 0.5
O B:HOH493 2.1 22.1 1.0
OE2 B:GLU95 2.5 16.9 0.5
CD B:GLU95 2.5 16.7 0.5
O B:HOH550 2.5 25.4 1.0
CD B:GLU95 2.8 11.5 0.5
CD2 A:HIS17 3.0 11.4 1.0
CE1 A:HIS17 3.0 13.2 1.0
OE2 B:GLU95 3.0 11.8 0.5
CG B:GLU95 4.0 14.7 0.5
O A:HOH566 4.0 36.8 1.0
ND1 A:HIS17 4.1 13.2 1.0
CG A:HIS17 4.1 9.6 1.0
O B:HOH521 4.2 34.4 1.0
OG1 B:THR92 4.2 16.1 1.0
O A:HOH422 4.2 13.7 1.0
CG1 A:VAL77 4.3 12.1 1.0
CG B:GLU95 4.3 11.2 0.5
O B:HOH450 4.4 27.9 1.0
O A:HOH483 4.4 21.9 1.0
CA B:THR92 4.6 13.6 1.0
CB B:GLU95 4.8 11.6 0.5
CB B:GLU95 4.8 11.9 0.5
CB B:THR92 4.9 14.5 1.0
CG2 A:VAL77 4.9 12.3 1.0
CG2 B:THR92 4.9 17.9 1.0

Zinc binding site 6 out of 6 in 2gyq

Go back to Zinc Binding Sites List in 2gyq
Zinc binding site 6 out of 6 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn408

b:12.4
occ:0.80
OE2 B:GLU12 1.9 17.1 1.0
NE2 B:HIS133 2.0 14.0 1.0
O A:HOH498 2.0 17.3 1.0
CD B:GLU12 2.7 17.6 1.0
OE1 B:GLU12 2.8 16.9 1.0
CE1 B:HIS133 2.9 14.0 1.0
CD2 B:HIS133 3.0 12.3 1.0
CB A:ALA168 3.7 24.4 1.0
O A:SER169 4.0 18.0 1.0
O B:HOH502 4.0 27.8 1.0
ND1 B:HIS133 4.0 13.4 1.0
CG B:HIS133 4.1 10.9 1.0
CG B:GLU12 4.1 17.2 1.0
CD2 B:LEU70 4.5 12.9 1.0
CA A:ALA168 4.8 22.1 1.0
N A:SER169 4.9 19.9 1.0
C A:ALA168 4.9 21.2 1.0
C A:SER169 4.9 18.8 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: Wed Dec 16 03:29:41 2020

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