Atomistry » Zinc » PDB 3dsv-3e2c » 3dza
Atomistry »
  Zinc »
    PDB 3dsv-3e2c »
      3dza »

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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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

Go back to Zinc Binding Sites List in 3dza
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: Wed Dec 16 04:14:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy