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Manganese in PDB 1yd2: Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation, PDB code: 1yd2 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 (°) 55.817, 55.817, 111.352, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.2

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 Y19F Bound to the Catalytic Divalent Cation (pdb code 1yd2). 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 Y19F Bound to the Catalytic Divalent Cation, PDB code: 1yd2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1yd2

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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 Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2001

b:20.3
occ:1.00
 OE2 A:GLU76 2.2 17.8 1.0
O A:HOH2036 2.2 24.9 1.0
O A:HOH2010 2.2 18.6 1.0
O A:HOH2029 2.3 22.6 1.0
O A:HOH2037 2.3 22.9 1.0
O A:HOH2008 2.4 18.1 1.0
CD A:GLU76 3.2 17.8 1.0
OE1 A:GLU76 3.5 21.1 1.0
O A:HOH2194 4.3 64.0 1.0
O A:HOH2034 4.3 30.8 1.0
CA A:GLY31 4.4 16.9 1.0
OH A:TYR29 4.4 19.0 1.0
O A:HOH2179 4.5 62.4 1.0
O A:ILE30 4.5 16.4 1.0
O A:HOH2092 4.5 49.2 1.0
CG A:GLU76 4.5 16.5 1.0
O A:HOH2011 4.6 20.3 1.0
O A:HOH2077 4.6 45.2 1.0
O A:HOH2017 4.6 23.1 1.0
N A:LYS32 4.6 17.9 1.0
CD1 A:ILE80 4.8 19.9 1.0
O A:HOH2148 5.0 68.2 1.0
C A:GLY31 5.0 17.4 1.0

Manganese binding site 2 out of 5 in 1yd2

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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 Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:41.6
occ:1.00
 O A:HOH2117 3.1 56.0 1.0
O A:HOH2143 3.2 61.0 1.0
N A:LEU61 3.3 19.3 1.0
CE A:LYS4 3.6 35.0 1.0
NZ A:LYS4 3.6 38.4 1.0
O A:LEU61 3.8 21.1 1.0
CA A:GLU60 3.8 20.7 1.0
CD A:LYS4 3.9 32.9 1.0
C A:GLU60 4.1 19.8 1.0
O A:HOH2084 4.1 62.3 1.0
CG1 A:ILE5 4.2 23.5 1.0
CG A:LYS4 4.2 31.9 1.0
CG A:GLU60 4.3 22.7 1.0
CA A:LEU61 4.3 19.3 1.0
CB A:LEU61 4.5 19.0 1.0
C A:LEU61 4.5 19.8 1.0
CB A:GLU60 4.5 20.7 1.0
O A:LYS4 4.6 26.7 1.0
O A:HOH2141 4.6 67.3 1.0
C A:LYS4 4.7 26.6 1.0
N A:ILE5 4.8 24.7 1.0
CB A:LYS4 4.8 28.7 1.0
O A:ASP59 4.8 22.8 1.0
CA A:ILE5 4.8 24.0 1.0
O A:HOH2098 4.8 54.9 1.0
CD A:LYS8 4.8 32.5 1.0
N A:GLU60 4.9 21.1 1.0
O A:HOH2174 5.0 51.0 1.0

Manganese binding site 3 out of 5 in 1yd2

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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 Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2004

b:48.8
occ:1.00
 O A:HOH2129 2.2 38.4 1.0
O A:HOH2136 2.2 46.1 1.0
O A:HOH2139 2.3 46.4 1.0
O A:HOH2155 2.4 51.8 1.0
N A:GLU49 4.4 20.0 1.0
CG A:GLU49 4.4 24.5 1.0
O A:HOH2132 4.5 54.5 1.0
CA A:THR48 4.6 20.7 1.0
O A:HOH2013 4.7 22.3 1.0
O A:HOH2181 4.8 74.1 1.0
O A:GLN47 4.9 22.4 1.0

Manganese binding site 4 out of 5 in 1yd2

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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 Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2005

b:47.3
occ:1.00
 OE1 A:GLU60 2.1 29.1 1.0
O A:HOH2069 2.8 42.7 1.0
CD A:GLU60 3.2 24.1 1.0
OE2 A:GLU60 3.6 26.2 1.0
O A:HOH2098 3.8 54.9 1.0
NZ A:LYS22 4.1 31.3 1.0
CG A:GLU60 4.5 22.7 1.0
O A:HOH2104 4.5 52.4 1.0
OE1 A:GLU62 4.7 30.7 1.0
CD A:LYS22 4.8 24.0 1.0
CE A:LYS22 4.8 27.5 1.0

Manganese binding site 5 out of 5 in 1yd2

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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 Y19F Bound to the 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 Y19F Bound to the Catalytic Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2006

b:36.1
occ:1.00
 NH2 A:ARG6 3.3 28.7 1.0
O A:HOH2078 3.3 51.4 1.0
N A:MET1 3.4 23.5 1.0
CB A:MET1 3.9 23.4 1.0
O A:MET1 3.9 25.7 1.0
CA A:MET1 4.1 24.3 1.0
CZ A:ARG6 4.2 29.0 1.0
NE A:ARG6 4.2 28.8 1.0
C A:MET1 4.5 25.1 1.0
O A:HOH2099 4.7 59.0 1.0
OE2 A:GLU56 4.8 22.8 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: Sat Oct 5 13:10:40 2024

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