Zinc in PDB 4ntm: Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)

Enzymatic activity of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)

All present enzymatic activity of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein):
4.1.2.50;

Protein crystallography data

The structure of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein), PDB code: 4ntm was solved by V.Bandarian, Z.D.Miles, Roberts S.A., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.92 / 2.05
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.297, 111.297, 126.047, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) (pdb code 4ntm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein), PDB code: 4ntm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ntm

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Zinc binding site 1 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:63.0
occ:1.00
 O6B A:2K8202 2.0 65.3 1.0
NE2 A:HIS33 2.1 96.9 1.0
NE2 A:HIS31 2.1 0.2 1.0
NE2 A:HIS16 2.1 0.0 1.0
CD2 A:HIS33 2.8 91.3 1.0
C6A A:2K8202 2.9 67.8 1.0
CD2 A:HIS31 3.0 0.2 1.0
CD2 A:HIS16 3.0 97.7 1.0
CE1 A:HIS16 3.1 97.5 1.0
CE1 A:HIS31 3.1 0.2 1.0
O6A A:2K8202 3.2 66.8 1.0
CE1 A:HIS33 3.2 92.2 1.0
OE1 A:GLU110 3.7 80.0 1.0
CG A:HIS33 4.1 87.8 1.0
CD A:GLU110 4.1 77.5 1.0
CG A:HIS31 4.1 0.9 1.0
ND1 A:HIS31 4.1 0.5 1.0
ND1 A:HIS16 4.2 97.1 1.0
CG A:HIS16 4.2 95.8 1.0
ND1 A:HIS33 4.2 89.3 1.0
C6 A:2K8202 4.2 66.4 1.0
NE2 C:HIS71 4.2 82.0 1.0
CG A:GLU110 4.5 74.9 1.0
N5 A:2K8202 4.5 66.4 1.0
CD2 C:HIS71 4.7 83.5 1.0
OE2 A:GLU110 4.7 77.8 1.0

Zinc binding site 2 out of 6 in 4ntm

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Zinc binding site 2 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:35.4
occ:1.00
 O6B B:2K8202 1.9 33.7 1.0
NE2 B:HIS16 2.1 44.0 1.0
NE2 B:HIS31 2.1 50.6 1.0
NE2 B:HIS33 2.1 47.8 1.0
C6A B:2K8202 2.9 41.0 1.0
CE1 B:HIS31 3.0 47.9 1.0
CE1 B:HIS16 3.0 41.2 1.0
CD2 B:HIS33 3.0 43.5 1.0
CD2 B:HIS31 3.1 48.4 1.0
CD2 B:HIS16 3.1 41.7 1.0
CE1 B:HIS33 3.2 47.1 1.0
O6A B:2K8202 3.3 47.2 1.0
OE2 B:GLU110 3.4 46.6 1.0
CD B:GLU110 3.9 47.0 1.0
ND1 B:HIS31 4.1 47.9 1.0
ND1 B:HIS16 4.1 39.5 1.0
OE1 B:GLU110 4.1 49.4 1.0
CG B:HIS33 4.2 43.8 1.0
CG B:HIS31 4.2 47.8 1.0
C6 B:2K8202 4.2 39.7 1.0
ND1 B:HIS33 4.2 46.1 1.0
CG B:HIS16 4.2 39.5 1.0
N5 B:2K8202 4.3 40.4 1.0
NE2 D:HIS71 4.4 47.4 1.0
O B:HOH332 4.6 45.3 1.0
CD2 D:HIS71 4.7 47.0 1.0
CB B:CYS27 5.0 52.5 0.5
SG B:CYS27 5.0 55.0 0.5
CG B:GLU110 5.0 45.5 1.0

Zinc binding site 3 out of 6 in 4ntm

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Zinc binding site 3 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:57.1
occ:1.00
 O6A C:2K8202 2.0 50.0 1.0
NE2 C:HIS31 2.1 93.1 1.0
NE2 C:HIS33 2.1 93.2 1.0
NE2 C:HIS16 2.1 95.8 1.0
CE1 C:HIS16 2.8 93.0 1.0
C6A C:2K8202 2.9 51.9 1.0
CD2 C:HIS33 3.0 88.8 1.0
CE1 C:HIS31 3.0 92.5 1.0
CD2 C:HIS31 3.1 89.0 1.0
O6B C:2K8202 3.1 55.5 1.0
CE1 C:HIS33 3.2 89.0 1.0
CD2 C:HIS16 3.3 92.5 1.0
OE1 C:GLU110 3.7 77.0 1.0
ND1 C:HIS16 4.0 93.2 1.0
ND1 C:HIS31 4.1 92.2 1.0
CG C:HIS33 4.2 85.5 1.0
C6 C:2K8202 4.2 53.3 1.0
CG C:HIS31 4.2 89.5 1.0
ND1 C:HIS33 4.2 86.4 1.0
CG C:HIS16 4.3 92.2 1.0
CE1 A:HIS71 4.3 84.2 1.0
CD C:GLU110 4.4 76.4 1.0
N5 C:2K8202 4.5 54.0 1.0
ND1 A:HIS71 4.7 85.4 1.0

Zinc binding site 4 out of 6 in 4ntm

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Zinc binding site 4 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:40.3
occ:1.00
 O6A D:2K8202 2.0 41.2 1.0
NE2 D:HIS33 2.0 49.2 1.0
NE2 D:HIS31 2.1 52.5 1.0
NE2 D:HIS16 2.1 54.5 1.0
C6A D:2K8202 2.9 47.7 1.0
CE1 D:HIS33 2.9 47.2 1.0
CD2 D:HIS31 3.0 49.3 1.0
CE1 D:HIS31 3.0 50.6 1.0
CE1 D:HIS16 3.1 52.3 1.0
CD2 D:HIS16 3.1 50.8 1.0
CD2 D:HIS33 3.1 46.2 1.0
O6B D:2K8202 3.3 47.6 1.0
OE1 D:GLU110 3.3 56.6 1.0
CD D:GLU110 4.0 55.2 1.0
ND1 D:HIS33 4.1 46.1 1.0
ND1 D:HIS31 4.1 49.2 1.0
C6 D:2K8202 4.1 48.3 1.0
CG D:HIS31 4.1 48.1 1.0
ND1 D:HIS16 4.2 52.2 1.0
CG D:HIS33 4.2 45.3 1.0
CG D:HIS16 4.2 50.0 1.0
N5 D:2K8202 4.3 49.6 1.0
OE2 D:GLU110 4.4 57.0 1.0
NE2 B:HIS71 4.5 46.2 1.0
CD2 B:HIS71 4.7 45.6 1.0
CG D:GLU110 4.9 53.9 1.0

Zinc binding site 5 out of 6 in 4ntm

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Zinc binding site 5 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:33.2
occ:1.00
 O6A E:2K8202 2.0 34.5 1.0
NE2 E:HIS31 2.1 43.1 1.0
NE2 E:HIS33 2.1 42.9 1.0
NE2 E:HIS16 2.1 42.3 1.0
C6A E:2K8202 2.9 33.5 1.0
CE1 E:HIS31 3.0 42.4 1.0
CD2 E:HIS33 3.0 41.1 1.0
CD2 E:HIS31 3.0 42.2 1.0
CD2 E:HIS16 3.1 40.2 1.0
CE1 E:HIS16 3.1 40.0 1.0
CE1 E:HIS33 3.1 41.4 1.0
O6B E:2K8202 3.1 34.5 1.0
OE1 E:GLU110 3.5 43.8 1.0
CD E:GLU110 4.0 41.6 1.0
ND1 E:HIS31 4.1 42.0 1.0
CG E:HIS31 4.1 41.9 1.0
CG E:HIS33 4.2 40.6 1.0
ND1 E:HIS16 4.2 39.6 1.0
ND1 E:HIS33 4.2 41.0 1.0
C6 E:2K8202 4.2 31.6 1.0
CG E:HIS16 4.2 39.9 1.0
OE2 E:GLU110 4.3 41.8 1.0
N5 E:2K8202 4.4 32.7 1.0
NE2 F:HIS71 4.4 44.2 1.0
CD2 F:HIS71 4.7 44.1 1.0
CG E:GLU110 4.8 40.5 1.0
O F:HOH301 5.0 37.9 1.0

Zinc binding site 6 out of 6 in 4ntm

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Zinc binding site 6 out of 6 in the Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Qued Soaked with Sepiapterin (Selenomethionine Substituted Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:41.5
occ:1.00
 O6B F:2K8202 2.0 43.2 1.0
NE2 F:HIS16 2.1 53.0 1.0
NE2 F:HIS31 2.1 57.5 1.0
NE2 F:HIS33 2.1 54.4 1.0
C6A F:2K8202 2.7 43.8 1.0
O6A F:2K8202 2.9 45.6 1.0
CD2 F:HIS33 2.9 49.8 1.0
CE1 F:HIS31 3.0 55.3 1.0
CE1 F:HIS16 3.0 50.9 1.0
CD2 F:HIS16 3.1 49.8 1.0
CD2 F:HIS31 3.1 53.8 1.0
CE1 F:HIS33 3.2 52.8 1.0
OE1 F:GLU110 3.6 56.3 1.0
CD F:GLU110 4.0 56.2 1.0
ND1 F:HIS31 4.1 53.8 1.0
CG F:HIS33 4.1 48.7 1.0
C6 F:2K8202 4.1 47.6 1.0
ND1 F:HIS16 4.1 49.7 1.0
CG F:HIS31 4.2 53.0 1.0
CG F:HIS16 4.2 48.6 1.0
ND1 F:HIS33 4.2 51.2 1.0
N5 F:2K8202 4.5 49.8 1.0
NE2 E:HIS71 4.5 53.3 1.0
CG F:GLU110 4.6 54.5 1.0
OE2 F:GLU110 4.6 57.9 1.0
CD2 E:HIS71 4.7 53.2 1.0
SG F:CYS27 4.9 64.2 0.5

Reference:

Z.D.Miles, S.A.Roberts, R.M.Mccarty, V.Bandarian. Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-Tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity Within the Tunnel-Fold Superfamily. J.Biol.Chem. V. 289 23641 2014.
ISSN: ISSN 0021-9258
PubMed: 24990950
DOI: 10.1074/JBC.M114.555680
Page generated: Wed Dec 16 05:37:40 2020

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