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Manganese in PDB 1yd3: Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation

Protein crystallography data

The structure of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation, PDB code: 1yd3 was solved by J.J.Truglio, B.Rhau, D.L.Croteau, L.Wang, M.Skorvaga, E.Karakas, M.J.Dellavecchia, H.Wang, B.Van Houten, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.094, 56.094, 111.491, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation (pdb code 1yd3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation, PDB code: 1yd3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1yd3

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Manganese binding site 1 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2001

b:21.8
occ:1.00
OE2 A:GLU76 2.2 19.2 1.0
O A:HOH2092 2.2 20.7 1.0
O A:HOH2035 2.2 24.4 1.0
O A:HOH2178 2.2 26.8 1.0
O A:HOH2045 2.2 25.5 1.0
O A:HOH2179 2.4 18.4 1.0
CD A:GLU76 3.2 19.0 1.0
OE1 A:GLU76 3.5 21.9 1.0
O A:HOH2138 4.3 57.0 1.0
O A:HOH2114 4.3 54.6 1.0
CA A:GLY31 4.4 16.3 1.0
O A:HOH2124 4.4 56.3 1.0
O A:HOH2031 4.4 29.3 1.0
O A:HOH2082 4.5 49.6 1.0
O A:ILE30 4.5 16.0 1.0
OH A:TYR29 4.5 19.1 1.0
CG A:GLU76 4.5 17.3 1.0
N A:LYS32 4.6 17.7 1.0
O A:HOH2015 4.7 24.0 1.0
CD1 A:ILE80 4.8 18.5 1.0
C A:GLY31 5.0 17.2 1.0

Manganese binding site 2 out of 5 in 1yd3

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Manganese binding site 2 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:39.4
occ:1.00
O A:HOH2105 3.1 49.2 1.0
N A:LEU61 3.4 19.5 1.0
O A:LEU61 3.9 20.8 1.0
CA A:GLU60 3.9 20.8 1.0
C A:GLU60 4.1 19.9 1.0
CE A:LYS4 4.1 34.0 1.0
CG1 A:ILE5 4.2 23.2 1.0
CG A:LYS4 4.2 31.0 1.0
CA A:LEU61 4.3 19.6 1.0
CG A:GLU60 4.3 22.9 1.0
CD A:LYS4 4.4 31.4 1.0
CB A:LEU61 4.5 19.8 1.0
C A:LEU61 4.5 19.6 1.0
CB A:GLU60 4.6 21.2 1.0
O A:LYS4 4.6 26.0 1.0
CD A:LYS8 4.6 29.3 1.0
O A:HOH2118 4.7 61.0 1.0
NZ A:LYS4 4.7 36.5 1.0
C A:LYS4 4.7 26.0 1.0
N A:ILE5 4.8 24.4 1.0
CA A:ILE5 4.8 23.7 1.0
CB A:LYS4 4.8 28.1 1.0
O A:ASP59 4.8 22.5 1.0
N A:GLU60 4.9 21.1 1.0
O A:HOH2095 5.0 40.0 1.0

Manganese binding site 3 out of 5 in 1yd3

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Manganese binding site 3 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2004

b:48.4
occ:1.00
O A:HOH2155 2.1 45.3 1.0
OE1 A:GLU49 2.2 29.5 1.0
O A:HOH2107 2.2 44.4 1.0
O A:HOH2112 2.2 46.1 1.0
O A:HOH2156 2.5 55.9 1.0
CD A:GLU49 3.1 29.7 1.0
OE2 A:GLU49 3.2 33.8 1.0
N A:GLU49 4.5 19.0 1.0
O A:HOH2154 4.5 51.4 1.0
CG A:GLU49 4.5 24.2 1.0
CA A:THR48 4.6 20.0 1.0
O A:HOH2011 4.7 23.2 1.0
CB A:THR48 5.0 20.5 1.0

Manganese binding site 4 out of 5 in 1yd3

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Manganese binding site 4 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2005

b:46.7
occ:1.00
OE1 A:GLU60 2.2 29.3 1.0
O A:HOH2174 2.2 39.2 1.0
O A:HOH2132 2.3 46.5 1.0
O A:HOH2090 2.8 42.3 1.0
CD A:GLU60 3.2 24.0 1.0
OE2 A:GLU60 3.6 26.1 1.0
NZ A:LYS22 4.0 30.7 1.0
O A:HOH2108 4.5 52.9 1.0
CG A:GLU60 4.5 22.9 1.0
CD A:LYS22 4.7 23.3 1.0
OE1 A:GLU62 4.8 30.0 1.0
CE A:LYS22 4.8 27.6 1.0

Manganese binding site 5 out of 5 in 1yd3

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Manganese binding site 5 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2006

b:34.5
occ:1.00
NH2 A:ARG6 3.3 27.0 1.0
N A:MET1 3.4 23.5 1.0
O A:HOH2071 3.5 48.9 1.0
O A:HOH2040 3.6 33.4 1.0
O A:MET1 3.9 25.1 1.0
CB A:MET1 4.0 23.4 1.0
CA A:MET1 4.1 24.1 1.0
CZ A:ARG6 4.2 26.8 1.0
NE A:ARG6 4.3 26.4 1.0
C A:MET1 4.5 24.8 1.0
OE2 A:GLU56 4.8 23.0 1.0

Reference:

J.J.Truglio, B.Rhau, D.L.Croteau, L.Wang, M.Skorvaga, E.Karakas, M.J.Dellavecchia, H.Wang, B.Van Houten, C.Kisker. Structural Insights Into the First Incision Reaction During Nucleotide Excision Repair Embo J. V. 24 885 2005.
ISSN: ISSN 0261-4189
PubMed: 15692561
DOI: 10.1038/SJ.EMBOJ.7600568
Page generated: Tue Dec 15 03:58:21 2020

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