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Zinc in PDB 1f35: Crystal Structure of Murine Olfactory Marker Protein

Protein crystallography data

The structure of Crystal Structure of Murine Olfactory Marker Protein, PDB code: 1f35 was solved by P.C.Smith, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.270, 87.270, 164.100, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 24.7

Other elements in 1f35:

The structure of Crystal Structure of Murine Olfactory Marker Protein also contains other interesting chemical elements:

Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Murine Olfactory Marker Protein (pdb code 1f35). 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 Murine Olfactory Marker Protein, PDB code: 1f35:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1f35

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Zinc binding site 1 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:42.6
occ:1.00
 OE2 A:GLU119 2.0 30.8 1.0
OD1 A:ASP116 2.0 43.5 1.0
CG A:ASP116 2.7 37.1 1.0
CD A:GLU119 2.8 37.4 1.0
OD2 A:ASP116 2.8 37.2 1.0
OE1 A:GLU119 3.0 44.2 1.0
ZN A:ZN302 3.1 61.3 1.0
O A:TRP117 3.2 37.5 1.0
O A:HOH619 3.9 38.9 1.0
N A:TRP117 4.1 32.7 1.0
O A:HOH677 4.1 60.3 1.0
CB A:ASP116 4.2 35.0 1.0
CG A:GLU119 4.3 38.7 1.0
C A:TRP117 4.3 33.3 1.0
CA A:ASP116 4.7 35.4 1.0
CZ2 A:TRP107 4.8 35.6 1.0
CA A:TRP117 4.9 31.8 1.0
C A:ASP116 4.9 33.7 1.0

Zinc binding site 2 out of 10 in 1f35

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Zinc binding site 2 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:46.7
occ:1.00
 O1 A:CAC351 1.5 62.1 1.0
OD1 A:ASP90 2.1 45.0 1.0
O A:HOH556 2.4 19.0 1.0
OD2 A:ASP90 2.5 39.9 1.0
CG A:ASP90 2.6 41.7 1.0
AS A:CAC351 3.2 56.9 1.0
C1 A:CAC351 3.8 49.9 1.0
C2 A:CAC351 4.1 55.8 1.0
CB A:ASP90 4.1 40.0 1.0
O A:HOH629 4.3 45.5 1.0
O2 A:CAC351 4.6 64.1 1.0
CA A:ASP90 4.8 41.5 1.0
N A:ASP90 4.9 44.9 1.0
OH A:TYR140 4.9 41.0 1.0

Zinc binding site 3 out of 10 in 1f35

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Zinc binding site 3 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:73.4
occ:1.00
 O A:HOH561 2.1 44.8 1.0
OD2 A:ASP121 2.2 53.1 1.0
O A:HOH502 2.4 31.5 1.0
CG A:ASP121 2.9 52.7 1.0
OD1 A:ASP121 3.0 57.1 1.0
O A:HOH539 3.2 50.1 1.0
O A:HOH509 3.6 67.9 1.0
O A:HOH612 4.2 46.4 1.0
CB A:ASP121 4.4 47.9 1.0
CB A:PRO102 4.7 36.2 1.0

Zinc binding site 4 out of 10 in 1f35

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Zinc binding site 4 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:68.9
occ:1.00
 O2 A:CAC351 1.7 64.1 1.0
OD1 A:ASP20 1.9 53.4 1.0
OD1 A:ASP18 2.2 51.4 1.0
O A:HOH557 2.3 32.4 1.0
CG A:ASP20 2.7 53.1 1.0
OD2 A:ASP20 3.0 58.2 1.0
CG A:ASP18 3.0 48.0 1.0
OD2 A:ASP18 3.2 49.4 1.0
O A:HOH629 3.2 45.5 1.0
AS A:CAC351 3.5 56.9 1.0
N A:LEU21 3.9 43.3 1.0
NH1 A:ARG54 4.1 60.3 1.0
CB A:ASP20 4.1 46.8 1.0
O A:HOH536 4.2 53.0 1.0
CB A:LEU21 4.3 34.8 1.0
CB A:ASP18 4.4 40.8 1.0
O1 A:CAC351 4.4 62.1 1.0
C1 A:CAC351 4.5 49.9 1.0
N A:ASP20 4.5 42.9 1.0
C A:ASP20 4.6 46.2 1.0
CA A:ASP20 4.6 46.4 1.0
CA A:LEU21 4.6 39.1 1.0
CA A:ASP18 4.8 39.6 1.0
C2 A:CAC351 4.9 55.8 1.0
C A:ASP18 4.9 41.2 1.0

Zinc binding site 5 out of 10 in 1f35

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Zinc binding site 5 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:61.7
occ:1.00
 OE1 A:GLU3 2.2 80.4 1.0
O A:HOH610 2.7 34.7 1.0
OE2 A:GLU3 2.8 82.0 1.0
CD A:GLU3 2.9 79.6 1.0
O A:HOH646 3.0 54.0 1.0
O A:HOH645 4.2 43.2 1.0
O A:HOH611 4.3 48.6 1.0
CG A:GLU3 4.3 77.5 1.0
CB A:GLU3 4.9 77.6 1.0
CA A:GLU3 4.9 79.3 1.0

Zinc binding site 6 out of 10 in 1f35

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Zinc binding site 6 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:61.3
occ:1.00
 O A:HOH677 1.5 60.3 1.0
OE1 A:GLU119 2.2 44.2 1.0
ZN A:ZN301 3.1 42.6 1.0
O A:HOH503 3.2 68.3 1.0
CD A:GLU119 3.2 37.4 1.0
OE2 A:GLU119 3.6 30.8 1.0
O A:TRP117 3.9 37.5 1.0
N A:GLU119 4.5 39.0 1.0
CG A:GLU119 4.5 38.7 1.0
CB A:GLU119 4.8 40.0 1.0
CA A:ASN118 4.9 38.9 1.0
OD1 A:ASP116 5.0 43.5 1.0

Zinc binding site 7 out of 10 in 1f35

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Zinc binding site 7 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:39.5
occ:1.00
 OE2 B:GLU1119 2.0 31.5 1.0
OD1 B:ASP1116 2.0 36.0 1.0
CG B:ASP1116 2.7 35.7 1.0
OD2 B:ASP1116 2.8 39.4 1.0
CD B:GLU1119 2.8 34.2 1.0
OE1 B:GLU1119 3.0 40.2 1.0
ZN B:ZN309 3.0 54.7 1.0
O B:TRP1117 3.1 38.6 1.0
O B:HOH641 3.9 34.7 1.0
N B:TRP1117 4.0 33.8 1.0
CB B:ASP1116 4.2 31.7 1.0
C B:TRP1117 4.2 33.6 1.0
CG B:GLU1119 4.3 33.0 1.0
CZ2 B:TRP1107 4.6 33.8 1.0
CA B:ASP1116 4.7 36.1 1.0
CA B:TRP1117 4.8 34.3 1.0
C B:ASP1116 4.8 35.2 1.0
CH2 B:TRP1107 4.9 37.1 1.0

Zinc binding site 8 out of 10 in 1f35

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Zinc binding site 8 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn309

b:54.7
occ:1.00
 OE1 B:GLU1119 2.2 40.2 1.0
ZN B:ZN308 3.0 39.5 1.0
CD B:GLU1119 3.3 34.2 1.0
OE2 B:GLU1119 3.6 31.5 1.0
O B:TRP1117 3.8 38.6 1.0
N B:GLU1119 4.4 37.2 1.0
CG B:GLU1119 4.6 33.0 1.0
CA B:ASN1118 4.7 38.5 1.0
CB B:GLU1119 4.9 34.4 1.0
C B:TRP1117 4.9 33.6 1.0
OD1 B:ASP1116 5.0 36.0 1.0

Zinc binding site 9 out of 10 in 1f35

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Zinc binding site 9 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn310

b:0.3
occ:1.00
 OE1 A:GLU150 2.6 74.8 1.0
OD1 B:ASP1056 2.8 70.1 1.0
CD A:GLU150 3.2 67.1 1.0
OE2 A:GLU150 3.3 71.7 1.0
CG B:ASP1056 3.4 66.3 1.0
OD2 B:ASP1056 3.7 72.4 1.0
O B:HOH667 4.0 52.1 1.0
CG A:GLU150 4.5 59.2 1.0
CB B:ASP1056 4.7 55.0 1.0
O A:HOH636 4.7 50.6 1.0

Zinc binding site 10 out of 10 in 1f35

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Zinc binding site 10 out of 10 in the Crystal Structure of Murine Olfactory Marker Protein


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 Murine Olfactory Marker Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:45.6
occ:1.00
 O B:HOH678 1.5 47.6 1.0
OE2 A:GLU147 1.9 46.9 1.0
OD1 B:ASP1018 2.1 46.6 1.0
OD1 B:ASP1020 2.2 51.7 1.0
CG B:ASP1018 2.8 45.9 1.0
CD A:GLU147 2.8 42.5 1.0
OD2 B:ASP1018 2.8 45.4 1.0
OE1 A:GLU147 3.0 43.7 1.0
CG B:ASP1020 3.2 49.5 1.0
OD2 B:ASP1020 3.4 47.8 1.0
NH1 B:ARG1054 3.6 54.7 1.0
O A:HOH550 4.1 40.7 1.0
O B:HOH609 4.2 64.2 1.0
N B:LEU1021 4.2 41.8 1.0
CB B:ASP1018 4.2 40.6 1.0
CG A:GLU147 4.2 36.2 1.0
CB B:LEU1021 4.3 36.1 1.0
CB B:ASP1020 4.6 47.0 1.0
CA B:ASP1018 4.7 40.6 1.0
N B:ASP1020 4.8 43.7 1.0
CA B:LEU1021 4.8 39.6 1.0
C B:ASP1020 4.9 45.4 1.0
CZ B:ARG1054 4.9 53.5 1.0
C B:ASP1018 4.9 41.4 1.0
CA B:ASP1020 4.9 46.7 1.0

Reference:

P.C.Smith, S.Firestein, J.F.Hunt. The Crystal Structure of the Olfactory Marker Protein at 2.3 A Resolution. J.Mol.Biol. V. 319 807 2002.
ISSN: ISSN 0022-2836
PubMed: 12054872
DOI: 10.1016/S0022-2836(02)00242-5
Page generated: Sun Oct 13 00:42:18 2024

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