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Zinc in PDB 3dza: Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution, PDB code: 3dza was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.207, 79.016, 137.990, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution (pdb code 3dza). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution, PDB code: 3dza:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3dza

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Zinc binding site 1 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.4
occ:1.00
 NE2 A:HIS77 2.1 12.1 1.0
O B:HOH624 2.1 23.7 1.0
O B:HOH614 2.1 23.8 1.0
O B:HOH597 2.2 21.4 1.0
O B:HOH590 2.3 21.8 1.0
OE1 B:GLU169 2.3 19.2 1.0
CE1 A:HIS77 3.0 13.5 1.0
CD B:GLU169 3.1 26.7 1.0
CD2 A:HIS77 3.1 10.6 1.0
OE2 B:GLU169 3.3 28.0 1.0
O B:HOH718 3.4 36.1 1.0
O B:HOH652 4.0 28.2 1.0
ND1 A:HIS77 4.1 9.0 1.0
O B:LEU216 4.1 27.2 1.0
CG A:HIS77 4.2 10.8 1.0
O B:LEU55 4.2 13.5 1.0
CG B:GLU169 4.5 20.9 1.0
O B:HOH716 4.5 36.4 1.0
CD2 B:LEU216 4.7 18.7 1.0
OE1 B:GLN56 4.9 31.0 0.7
O B:HOH766 4.9 46.3 1.0
NE2 B:GLN171 5.0 17.0 1.0

Zinc binding site 2 out of 10 in 3dza

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Zinc binding site 2 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:13.7
occ:1.00
 NE2 B:HIS77 2.1 12.1 1.0
OE2 A:GLU169 2.2 19.3 1.0
O A:HOH574 2.2 20.2 1.0
O A:HOH557 2.2 16.9 1.0
O A:HOH547 2.2 15.2 1.0
O B:HOH557 2.2 16.8 1.0
CE1 B:HIS77 3.0 11.9 1.0
CD A:GLU169 3.1 25.6 1.0
CD2 B:HIS77 3.1 10.7 1.0
O A:HOH687 3.4 33.5 1.0
OE1 A:GLU169 3.4 24.5 1.0
O A:LEU55 4.0 14.9 1.0
O A:HOH739 4.1 39.9 1.0
ND1 B:HIS77 4.2 8.4 1.0
CG B:HIS77 4.2 11.3 1.0
CG A:GLU169 4.5 22.6 1.0
O A:LEU216 4.5 24.3 1.0
O A:HOH596 4.5 21.7 1.0
CD2 A:LEU216 4.7 20.0 1.0

Zinc binding site 3 out of 10 in 3dza

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Zinc binding site 3 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:13.6
occ:1.00
 OD1 A:ASP212 2.0 13.2 1.0
O D:HOH764 2.1 18.6 1.0
O A:HOH578 2.1 20.6 1.0
OD1 D:ASP212 2.1 11.6 1.0
O A:HOH565 2.2 18.3 1.0
O D:HOH754 2.2 16.6 1.0
CG D:ASP212 3.0 17.0 1.0
CG A:ASP212 3.0 22.3 1.0
OD2 D:ASP212 3.3 23.9 1.0
OD2 A:ASP212 3.3 30.3 1.0
O A:SER213 4.1 11.5 1.0
O D:SER213 4.1 8.8 1.0
OE2 D:GLU214 4.1 13.8 0.7
CD A:LYS110 4.2 26.1 1.0
O A:HOH662 4.3 31.3 1.0
O A:HOH600 4.3 22.2 1.0
O D:HOH867 4.3 31.3 1.0
CB A:ASP212 4.4 12.3 1.0
CB D:ASP212 4.4 10.1 1.0
N A:SER213 4.4 9.4 1.0
N D:SER213 4.5 11.5 1.0
CG A:LYS110 4.5 28.3 1.0
OG D:SER213 4.7 7.0 0.5
CA A:ASP212 4.8 10.7 1.0
CA D:ASP212 4.8 9.4 1.0
OG A:SER213 4.8 8.4 0.5

Zinc binding site 4 out of 10 in 3dza

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Zinc binding site 4 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:17.7
occ:1.00
 OE1 B:GLU138 2.0 14.1 1.0
O B:HOH632 2.2 26.0 1.0
O B:HOH760 2.3 40.6 1.0
O B:HOH613 2.3 24.1 1.0
CD B:GLU138 2.8 12.5 1.0
OE2 B:GLU138 2.9 17.0 1.0
O B:HOH764 4.2 44.5 1.0
CG B:GLU138 4.2 8.8 1.0
O B:HOH679 4.4 30.6 1.0
CA B:PRO135 4.5 10.6 1.0
N B:PRO135 4.6 11.3 1.0
CG B:PRO135 4.6 11.9 1.0
CB B:GLU138 4.8 8.7 1.0
CD B:PRO135 4.8 10.0 1.0
C B:THR134 4.9 9.0 1.0
O B:HOH715 4.9 36.0 1.0
CB B:PRO135 4.9 11.7 1.0
O B:THR134 5.0 9.7 1.0

Zinc binding site 5 out of 10 in 3dza

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Zinc binding site 5 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:13.7
occ:1.00
 OD1 C:ASP212 2.0 14.7 1.0
OD1 B:ASP212 2.1 12.6 1.0
O B:HOH567 2.1 17.4 1.0
O B:HOH576 2.2 19.0 1.0
O B:HOH539 2.2 13.5 1.0
O C:HOH543 2.2 14.3 1.0
CG C:ASP212 3.0 13.2 1.0
CG B:ASP212 3.0 16.2 1.0
OD2 B:ASP212 3.3 20.8 1.0
OD2 C:ASP212 3.3 14.4 1.0
O B:SER213 4.0 12.1 1.0
O B:HOH591 4.1 21.6 1.0
O C:SER213 4.2 12.4 1.0
CB C:ASP212 4.3 10.6 1.0
O C:HOH558 4.4 16.4 1.0
O C:HOH613 4.4 25.2 1.0
N B:SER213 4.4 9.7 1.0
CB C:LYS110 4.4 18.5 1.0
O C:HOH582 4.4 21.4 1.0
CB B:ASP212 4.4 12.4 1.0
N C:SER213 4.5 11.4 1.0
OG B:SER213 4.7 10.3 0.5
CA C:ASP212 4.7 9.7 1.0
N C:LYS110 4.9 17.2 1.0
CA B:ASP212 4.9 10.6 1.0

Zinc binding site 6 out of 10 in 3dza

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Zinc binding site 6 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:13.4
occ:1.00
 O D:HOH761 1.8 18.3 1.0
NE2 C:HIS77 2.1 11.7 1.0
O D:HOH730 2.2 12.0 1.0
OE2 D:GLU169 2.2 15.9 1.0
O1 D:EDO16 2.2 16.1 1.0
O2 D:EDO16 2.2 19.7 1.0
C1 D:EDO16 3.0 24.7 1.0
CE1 C:HIS77 3.0 10.7 1.0
C2 D:EDO16 3.1 27.3 1.0
CD D:GLU169 3.1 19.3 1.0
CD2 C:HIS77 3.1 9.2 1.0
OE1 D:GLU169 3.3 25.2 1.0
O D:HOH831 3.8 26.2 1.0
ND1 C:HIS77 4.2 7.6 1.0
O D:LEU55 4.2 12.1 1.0
CG C:HIS77 4.3 8.2 1.0
O D:LEU216 4.4 23.8 1.0
CG D:GLU169 4.4 23.8 1.0
O D:HOH794 4.6 23.3 1.0
CD2 D:LEU216 4.8 13.8 1.0

Zinc binding site 7 out of 10 in 3dza

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Zinc binding site 7 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:17.5
occ:0.50
 OE2 C:GLU214 2.0 32.9 1.0
O C:HOH701 2.1 36.0 1.0
O C:HOH717 2.1 37.9 1.0
OD2 C:ASP108 2.2 29.0 1.0
CD C:GLU214 2.7 22.1 1.0
OE1 C:GLU214 2.8 38.3 1.0
CG C:ASP108 3.0 22.3 1.0
OD1 C:ASP108 3.1 17.3 1.0
O C:HOH721 3.8 39.0 1.0
NZ C:LYS106 4.0 16.1 1.0
O C:HOH576 4.1 21.3 1.0
CG C:GLU214 4.1 21.6 1.0
CB C:ASP108 4.4 20.3 1.0
O C:HOH669 5.0 31.2 1.0
O C:HOH582 5.0 21.4 1.0

Zinc binding site 8 out of 10 in 3dza

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Zinc binding site 8 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:20.6
occ:0.50
 O C:HOH657 2.1 30.7 1.0
OE1 C:GLU146 2.2 21.1 1.0
OE2 C:GLU146 2.4 29.9 1.0
CD C:GLU146 2.6 19.0 1.0
NE2 C:GLN142 3.9 26.7 0.5
O C:HOH599 4.0 24.9 1.0
CG C:GLU146 4.2 20.3 1.0
O C:HOH631 4.3 27.9 1.0
CD C:GLN142 4.9 17.3 0.5
CG C:GLN142 5.0 12.4 0.5
CB C:GLU146 5.0 14.5 1.0

Zinc binding site 9 out of 10 in 3dza

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Zinc binding site 9 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:13.8
occ:1.00
 O C:HOH566 2.0 18.8 1.0
NE2 D:HIS77 2.1 12.6 1.0
OE2 C:GLU169 2.1 17.2 1.0
O C:HOH557 2.2 16.1 1.0
O1 C:EDO13 2.2 15.7 1.0
O2 C:EDO13 2.3 16.9 1.0
CE1 D:HIS77 2.9 15.4 1.0
C2 C:EDO13 3.0 17.8 1.0
C1 C:EDO13 3.0 21.1 1.0
CD C:GLU169 3.1 26.0 1.0
CD2 D:HIS77 3.1 12.1 1.0
OE1 C:GLU169 3.4 22.8 1.0
O C:HOH669 4.1 31.2 1.0
O C:LEU55 4.1 12.4 1.0
ND1 D:HIS77 4.1 10.5 1.0
CG D:HIS77 4.2 12.7 1.0
O C:HOH734 4.4 39.8 1.0
CG C:GLU169 4.4 22.0 1.0
O C:HOH572 4.5 19.9 1.0
CD2 C:LEU216 4.6 19.6 1.0
OE1 C:GLN56 5.0 32.0 0.5

Zinc binding site 10 out of 10 in 3dza

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Zinc binding site 10 out of 10 in the Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Putative Membrane Protein of Unknown Function (Yfdx) From Klebsiella Pneumoniae Subsp. at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:18.0
occ:1.00
 OE1 D:GLU138 2.1 15.2 1.0
O D:HOH823 2.3 25.1 1.0
O D:HOH887 2.6 36.1 1.0
CD D:GLU138 2.7 14.9 1.0
OE2 D:GLU138 2.7 19.6 1.0
O D:HOH946 3.0 50.4 1.0
CG D:GLU138 4.2 10.4 1.0
O D:HOH702 4.2 38.0 1.0
O D:HOH873 4.2 32.9 1.0
CA D:PRO135 4.5 9.0 1.0
N D:PRO135 4.6 10.8 1.0
O D:HOH868 4.7 32.8 1.0
CB D:PRO135 4.7 12.3 1.0
CB D:GLU138 4.8 9.8 1.0
CD D:PRO135 4.9 11.5 1.0
C D:THR134 4.9 9.3 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Thu Oct 24 12:23:41 2024

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