Atomistry » Zinc » PDB 2bnn-2c6w » 2bp8
Atomistry »
  Zinc »
    PDB 2bnn-2c6w »
      2bp8 »

Zinc in PDB 2bp8: M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans

Protein crystallography data

The structure of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2bp8 was solved by M.A.Hough, M.J.Ellis, S.Antonyuk, R.W.Strange, G.Sawers, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 90.600, 90.600, 291.458, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 18.9

Other elements in 2bp8:

The structure of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2bp8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2bp8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 1 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1339

b:28.8
occ:1.00
 O A:HOH2417 2.0 20.7 1.0
NE2 A:HIS165 2.1 19.7 1.0
OD2 A:ASP167 2.1 18.1 1.0
OD1 A:ASP167 2.7 21.1 1.0
CG A:ASP167 2.8 19.2 1.0
CE1 A:HIS165 3.0 23.0 1.0
CD2 A:HIS165 3.1 21.4 1.0
OG1 A:THR234 3.9 18.1 1.0
ND1 A:HIS165 4.1 21.1 1.0
CG A:HIS165 4.2 20.1 1.0
CB A:ASP167 4.2 20.0 1.0
N A:THR234 4.3 19.6 1.0
CB A:THR234 4.3 19.1 1.0
O A:GLY232 4.4 20.0 1.0
N A:ASP167 4.8 18.7 1.0
CA A:THR234 4.9 19.0 1.0

Zinc binding site 2 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 2 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1340

b:41.3
occ:0.75
 O A:HOH2418 2.0 36.8 1.0
OD2 A:ASP73 2.2 22.8 1.0
O A:HOH2419 2.2 35.8 1.0
ND1 A:HIS70 2.6 23.4 1.0
CG A:ASP73 3.2 22.6 1.0
CG A:HIS70 3.4 20.9 1.0
CB A:HIS70 3.4 20.8 1.0
OD1 A:ASP73 3.4 24.1 1.0
CE1 A:HIS70 3.7 25.0 1.0
N A:HIS70 3.7 20.1 1.0
CA A:HIS70 4.2 20.0 1.0
NH1 A:ARG153 4.3 33.7 1.0
CB A:ASP73 4.6 21.2 1.0
C A:VAL69 4.6 18.9 1.0
CD2 A:HIS70 4.6 24.1 1.0
NH2 A:ARG153 4.6 32.6 1.0
O A:HOH2131 4.7 33.6 1.0
NE2 A:HIS70 4.7 24.0 1.0
CA A:VAL69 4.8 18.3 1.0
CG2 A:VAL33 4.9 23.4 1.0
CZ A:ARG153 4.9 32.5 1.0
O A:HOH2047 4.9 25.8 1.0
CD A:LYS31 5.0 34.2 1.0
O A:HIS70 5.0 20.3 1.0

Zinc binding site 3 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 3 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1341

b:40.6
occ:1.00
 O2 A:SO41344 1.8 56.1 1.0
O4 A:SO41345 2.0 45.0 1.0
NE2 A:HIS313 2.1 29.9 1.0
O A:HOH2420 2.4 20.5 1.0
CE1 A:HIS313 3.0 28.5 1.0
S A:SO41344 3.0 55.0 1.0
S A:SO41345 3.1 42.5 1.0
CD2 A:HIS313 3.1 26.1 1.0
O2 A:SO41345 3.2 46.6 1.0
O3 A:SO41344 3.4 57.2 1.0
O A:HOH2427 3.6 55.5 1.0
O4 A:SO41344 3.6 57.3 1.0
O3 A:SO41345 3.7 45.0 1.0
O A:HOH2429 3.8 46.5 1.0
O A:HOH2423 3.9 55.6 1.0
O1 A:SO41344 4.1 56.4 1.0
ND1 A:HIS313 4.1 28.2 1.0
CG A:HIS313 4.2 23.6 1.0
O1 A:SO41345 4.2 45.3 1.0
CB A:ALA296 5.0 19.7 1.0

Zinc binding site 4 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 4 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1342

b:41.5
occ:0.25
 O A:HOH2421 1.9 51.9 1.0
O A:HOH2422 2.1 50.8 1.0
OE1 A:GLU34 2.1 36.7 1.0
CD A:GLU34 3.0 31.6 1.0
OE2 A:GLU34 3.1 33.9 1.0
ND1 A:HIS8 3.1 38.5 1.0
CG A:HIS8 3.9 36.1 1.0
CB A:HIS8 4.0 35.6 1.0
CE1 A:HIS8 4.0 37.1 1.0
CG A:GLU34 4.4 27.4 1.0
O A:HOH2154 4.5 42.5 1.0
CE A:LYS10 4.9 41.1 1.0
CD2 A:HIS8 5.0 36.8 1.0

Zinc binding site 5 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 5 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1343

b:53.2
occ:0.50
 NE2 A:HIS8 2.1 38.2 1.0
CE1 A:HIS8 2.9 37.1 1.0
O A:ASP4 3.0 50.1 1.0
CD2 A:HIS8 3.2 36.8 1.0
C A:ASP4 3.7 49.5 1.0
O A:ALA3 3.9 51.4 1.0
CA A:ASP4 4.0 51.0 1.0
ND1 A:HIS8 4.0 38.5 1.0
O A:LEU6 4.1 37.8 1.0
CG A:HIS8 4.2 36.1 1.0
O A:HOH2155 4.4 33.3 1.0
O A:HOH2061 4.6 44.6 1.0
C A:ALA3 4.8 52.0 1.0
N A:ASP4 4.8 51.5 1.0
N A:LYS5 4.8 47.6 1.0
OD1 A:ASP4 5.0 54.3 1.0
O A:HOH2154 5.0 42.5 1.0

Zinc binding site 6 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 6 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1339

b:49.3
occ:0.75
 OD2 B:ASP73 2.1 25.4 1.0
O B:HOH2351 2.4 32.4 1.0
ND1 B:HIS70 2.6 26.3 1.0
CG B:ASP73 3.1 25.7 1.0
OD1 B:ASP73 3.3 28.7 1.0
CG B:HIS70 3.4 24.3 1.0
CB B:HIS70 3.5 23.4 1.0
CE1 B:HIS70 3.6 27.1 1.0
N B:HIS70 3.7 23.1 1.0
CA B:HIS70 4.2 22.9 1.0
NH1 B:ARG153 4.4 36.9 1.0
O B:HOH2105 4.4 31.1 1.0
CB B:ASP73 4.5 25.1 1.0
CD2 B:HIS70 4.6 26.9 1.0
C B:VAL69 4.6 22.8 1.0
NE2 B:HIS70 4.6 27.0 1.0
CG2 B:VAL33 4.8 28.1 1.0
CA B:VAL69 4.9 22.4 1.0
O B:HOH2042 4.9 33.8 1.0
NH2 B:ARG153 5.0 34.0 1.0
O B:HIS70 5.0 22.1 1.0

Zinc binding site 7 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 7 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1340

b:26.4
occ:1.00
 O B:HOH2352 1.9 24.6 1.0
OD2 B:ASP167 2.1 22.4 1.0
NE2 B:HIS165 2.1 20.5 1.0
OE2 A:GLU195 2.2 27.2 1.0
OD1 B:ASP167 2.5 23.1 1.0
CG B:ASP167 2.7 21.7 1.0
CD A:GLU195 2.8 23.1 1.0
OE1 A:GLU195 3.0 20.6 1.0
CE1 B:HIS165 3.0 21.7 1.0
CD2 B:HIS165 3.2 21.2 1.0
O A:HOH2291 3.6 40.2 1.0
OG1 B:THR234 4.0 22.3 1.0
ND1 B:HIS165 4.2 21.7 1.0
CG A:GLU195 4.2 21.8 1.0
CB B:ASP167 4.2 22.7 1.0
CB B:THR234 4.2 24.2 1.0
O A:HOH2285 4.3 25.9 1.0
CG B:HIS165 4.3 20.2 1.0
N B:THR234 4.3 24.3 1.0
O B:GLY232 4.6 26.6 1.0
N B:ASP167 4.7 21.6 1.0
CB A:ALA191 4.8 22.2 1.0
CA B:THR234 4.9 23.8 1.0
CA B:ASP167 5.0 22.9 1.0

Zinc binding site 8 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 8 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1341

b:33.2
occ:0.75
 NE2 B:HIS313 1.9 31.3 1.0
O2 B:SO41345 1.9 33.1 0.8
O3 B:SO41344 2.0 51.8 0.8
O B:HOH2353 2.5 28.8 1.0
O2 B:SO41344 2.6 52.3 0.8
CE1 B:HIS313 2.7 31.0 1.0
S B:SO41344 2.8 50.6 0.8
CD2 B:HIS313 3.1 29.2 1.0
S B:SO41345 3.1 31.0 0.8
O B:HOH2358 3.2 60.2 1.0
O3 B:SO41345 3.4 34.4 0.8
O4 B:SO41344 3.5 51.3 0.8
O4 B:SO41345 3.8 33.2 0.8
ND1 B:HIS313 3.9 31.2 1.0
O1 B:SO41344 4.0 51.4 0.8
O B:HOH2359 4.0 59.6 1.0
CG B:HIS313 4.1 25.9 1.0
O1 B:SO41345 4.2 35.6 0.8
CB B:ALA296 4.9 22.5 1.0

Zinc binding site 9 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 9 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1342

b:39.1
occ:0.25
 O B:HOH2354 1.9 50.0 1.0
O B:HOH2356 2.0 49.0 1.0
OE1 B:GLU34 2.2 38.9 1.0
O B:HOH2355 2.7 45.5 1.0
ND1 B:HIS8 3.0 44.3 1.0
CD B:GLU34 3.1 35.2 1.0
OE2 B:GLU34 3.4 37.7 1.0
CE1 B:HIS8 3.8 44.1 1.0
CG B:HIS8 4.0 42.9 1.0
CB B:HIS8 4.2 42.5 1.0
CG B:GLU34 4.5 31.3 1.0
O B:HOH2120 4.6 40.5 1.0
NE2 B:GLN76 4.7 29.8 1.0
NE2 B:HIS8 5.0 44.0 1.0

Zinc binding site 10 out of 10 in 2bp8

Go back to Zinc Binding Sites List in 2bp8
Zinc binding site 10 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1343

b:59.9
occ:0.50
 NE2 B:HIS8 2.2 44.0 1.0
CE1 B:HIS8 2.9 44.1 1.0
O B:ASP4 3.1 57.1 1.0
CD2 B:HIS8 3.2 43.3 1.0
O B:HOH2357 3.3 53.7 1.0
CA B:ASP4 3.6 58.0 1.0
C B:ASP4 3.7 56.9 1.0
O B:ALA3 3.8 58.7 1.0
O B:LEU6 4.0 47.0 1.0
NH2 B:ARG117 4.0 29.5 0.5
ND1 B:HIS8 4.0 44.3 1.0
CG B:HIS8 4.2 42.9 1.0
O B:HOH2161 4.4 21.3 0.5
CB B:ASP4 4.5 58.4 1.0
N B:ASP4 4.6 58.4 1.0
C B:ALA3 4.6 59.0 1.0
N B:LYS5 4.8 55.3 1.0

Reference:

M.A.Hough, M.J.Ellis, S.Antonyuk, R.W.Strange, G.Sawers, R.R.Eady, S.S.Hasnain. High Resolution Structural Studies of Mutants Provide Insights Into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase J.Mol.Biol. V. 350 300 2005.
ISSN: ISSN 0022-2836
PubMed: 15927201
DOI: 10.1016/J.JMB.2005.04.006
Page generated: Wed Oct 16 22:05:31 2024

Last articles

Mg in 3CC2
Mg in 3CCE
Mg in 3CC7
Mg in 3CC4
Mg in 3CB3
Mg in 3CC6
Mg in 3C9U
Mg in 3CBT
Mg in 3CBQ
Mg in 3CBG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy