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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

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Zinc binding site 1 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


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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

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Zinc binding site 2 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


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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

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Zinc binding site 3 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


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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

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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

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Zinc binding site 5 out of 10 in the M144Q Structure of Nitrite Reductase From Alcaligenes Xylosoxidans


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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

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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

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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

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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

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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

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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

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