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Manganese in PDB 1stx: Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+

Enzymatic activity of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+

All present enzymatic activity of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+:
3.1.21.4;

Protein crystallography data

The structure of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+, PDB code: 1stx was solved by N.C.Horton, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.710, 58.690, 82.100, 90.00, 107.70, 90.00
R / Rfree (%) 20.1 / 26.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ (pdb code 1stx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+, PDB code: 1stx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1stx

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Manganese binding site 1 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1003

b:38.1
occ:1.00
 OP1 D:DA7 1.9 56.6 1.0
OE2 A:GLU45 2.0 34.5 1.0
OD2 A:ASP74 2.3 22.4 1.0
O A:ILE91 2.5 24.5 1.0
P D:DA7 2.8 54.1 1.0
CD A:GLU45 3.1 34.5 1.0
OP3 D:DA7 3.1 54.5 1.0
CG A:ASP74 3.1 22.6 1.0
OD1 A:ASP74 3.3 24.1 1.0
OD2 A:ASP90 3.4 29.6 1.0
MN A:MN1004 3.4 48.2 1.0
C A:ILE91 3.5 24.0 1.0
OE1 A:GLU45 3.5 33.2 1.0
OP2 D:DA7 3.6 53.8 1.0
N A:ILE91 3.7 25.1 1.0
CA A:ILE91 4.0 25.6 1.0
CG A:ASP90 4.1 31.2 1.0
O5' D:DA7 4.2 51.5 1.0
O D:HOH312 4.2 37.9 1.0
CG A:GLU45 4.3 31.8 1.0
CB A:ILE91 4.3 27.9 1.0
O A:HOH1059 4.4 28.6 1.0
OD1 A:ASP90 4.5 35.2 1.0
CB A:ASP74 4.5 25.4 1.0
C5' D:DA7 4.6 46.5 1.0
C A:ASP90 4.6 25.7 1.0
CD A:LYS92 4.6 27.0 1.0
O A:HOH1186 4.7 31.3 1.0
N A:LYS92 4.7 23.4 1.0
NZ A:LYS92 4.7 29.1 1.0
C3' D:DA7 4.8 43.0 1.0
CE A:LYS92 4.8 26.9 1.0
CA A:ASP90 5.0 26.4 1.0

Manganese binding site 2 out of 6 in 1stx

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Manganese binding site 2 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1004

b:48.2
occ:1.00
 OP3 D:DA7 2.2 54.5 1.0
OD1 A:ASP74 2.2 24.1 1.0
OE1 A:GLU45 2.3 33.2 1.0
O A:HOH1187 2.4 32.5 1.0
O A:HOH1186 2.5 31.3 1.0
CG A:ASP74 3.1 22.6 1.0
CD A:GLU45 3.1 34.5 1.0
OE2 A:GLU45 3.2 34.5 1.0
MN A:MN1003 3.4 38.1 1.0
OD2 A:ASP74 3.5 22.4 1.0
P D:DA7 3.5 54.1 1.0
OP1 D:DA7 4.0 56.6 1.0
O D:HOH384 4.1 41.3 1.0
O5' D:DA7 4.4 51.5 1.0
C5' D:DA7 4.4 46.5 1.0
CB A:ASP74 4.4 25.4 1.0
OP2 D:DA7 4.5 53.8 1.0
O A:HOH1097 4.6 41.4 1.0
CG A:GLU45 4.6 31.8 1.0
OD2 B:ASP36 4.8 51.9 1.0
O A:HOH1134 4.9 32.8 1.0
CA A:ASP74 4.9 25.8 1.0

Manganese binding site 3 out of 6 in 1stx

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Manganese binding site 3 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1005

b:41.1
occ:1.00
 NE2 A:HIS71 2.2 32.9 1.0
OP1 F:DT11 2.4 39.8 1.0
O A:HOH1103 2.4 27.8 1.0
O A:HOH1133 2.5 23.4 1.0
CE1 A:HIS71 3.0 34.6 1.0
NE2 A:GLN68 3.3 45.0 1.0
CD2 A:HIS71 3.4 31.7 1.0
P F:DT11 3.8 33.6 1.0
CD A:GLN68 4.1 44.5 1.0
ND1 A:HIS71 4.2 34.3 1.0
C5' F:DT11 4.3 38.6 1.0
OE1 A:GLN68 4.3 45.6 1.0
O5' F:DT11 4.3 36.6 1.0
CG A:HIS71 4.4 32.6 1.0
N A:ASN120 4.4 22.2 1.0
O A:HOH1161 4.5 46.2 1.0
O3' F:DT10 4.5 35.0 1.0
O A:HOH1104 4.6 55.4 1.0
O A:THR118 4.6 25.9 1.0
CA A:ASN120 4.8 22.6 1.0
OP2 F:DT11 4.8 37.2 1.0
O A:HOH1081 4.9 45.7 1.0

Manganese binding site 4 out of 6 in 1stx

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Manganese binding site 4 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1007

b:64.1
occ:1.00
 O A:LYS102 1.9 37.6 1.0
NE2 A:HIS193 2.8 44.1 1.0
C A:LYS102 3.0 39.0 1.0
CD2 A:HIS193 3.5 41.6 1.0
CA A:LYS102 3.8 40.0 1.0
CB A:LYS102 3.8 40.5 1.0
CE1 A:HIS193 3.9 43.2 1.0
N A:ILE103 3.9 37.3 1.0
N A:LYS102 4.1 43.4 1.0
CA A:ILE103 4.1 35.5 1.0
O A:HOH1078 4.4 43.7 1.0
O A:HOH1030 4.4 50.8 1.0
CG A:GLU101 4.5 51.9 1.0
C A:ILE103 4.7 34.4 1.0
O A:HOH1060 4.7 25.0 1.0
OE2 A:GLU101 4.7 53.6 1.0
CG A:HIS193 4.7 39.5 1.0
O A:HOH1027 4.8 46.4 1.0
ND1 A:HIS193 4.9 41.5 1.0
C A:GLU101 4.9 47.1 1.0
N A:LYS104 5.0 33.6 1.0

Manganese binding site 5 out of 6 in 1stx

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Manganese binding site 5 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1002

b:38.4
occ:1.00
 OE1 B:GLU45 2.1 33.9 1.0
OD2 B:ASP74 2.2 30.1 1.0
OP2 F:DA7 2.3 48.7 1.0
O F:HOH276 2.3 35.8 1.0
O B:ILE91 2.4 25.5 1.0
CG B:ASP74 3.2 30.4 1.0
CD B:GLU45 3.2 36.5 1.0
P F:DA7 3.3 50.2 1.0
OP3 F:DA7 3.4 46.1 1.0
C B:ILE91 3.4 26.4 1.0
OD1 B:ASP74 3.4 33.8 1.0
O F:HOH63 3.6 16.9 1.0
N B:ILE91 3.6 26.9 1.0
OE2 B:GLU45 3.7 35.5 1.0
OD1 B:ASP90 3.7 27.1 1.0
CA B:ILE91 3.8 26.8 1.0
CB B:ILE91 3.9 28.5 1.0
CG B:ASP90 4.2 31.0 1.0
O5' F:DA7 4.3 47.3 1.0
OP1 F:DA7 4.4 49.8 1.0
CG B:GLU45 4.5 32.8 1.0
CB B:ASP74 4.5 29.8 1.0
C B:ASP90 4.5 26.5 1.0
OD2 B:ASP90 4.5 34.5 1.0
N B:LYS92 4.6 25.8 1.0
OP1 F:DT8 4.6 42.6 1.0
NZ B:LYS92 4.7 25.1 1.0
CG1 B:ILE91 4.7 29.9 1.0
O E:HOH277 4.8 29.1 1.0
O B:HOH1102 4.8 34.0 1.0
C5' F:DA7 4.8 44.4 1.0
CD B:LYS92 4.8 25.8 1.0
CA B:ASP90 5.0 27.3 1.0

Manganese binding site 6 out of 6 in 1stx

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Manganese binding site 6 out of 6 in the Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of the K38A Mutant of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1006

b:51.0
occ:1.00
 NE2 B:HIS71 2.2 41.2 1.0
O B:HOH1108 2.4 18.6 1.0
OP1 D:DT11 2.5 44.8 1.0
O B:HOH1109 2.7 52.9 1.0
CE1 B:HIS71 2.9 43.0 1.0
CD2 B:HIS71 3.4 39.2 1.0
NE2 B:GLN68 3.9 53.1 1.0
OE1 B:GLN68 4.0 55.7 1.0
P D:DT11 4.0 45.5 1.0
ND1 B:HIS71 4.1 41.2 1.0
O B:THR118 4.3 33.3 1.0
N B:ASN120 4.3 30.0 1.0
CD B:GLN68 4.4 53.7 1.0
CG B:HIS71 4.4 39.4 1.0
O B:HOH1052 4.5 56.4 1.0
C5' D:DT11 4.6 46.9 1.0
O3' D:DT10 4.7 44.5 1.0
O5' D:DT11 4.7 44.0 1.0
CA B:ASN120 4.8 30.0 1.0

Reference:

N.C.Horton, J.J.Perona. Dna Cleavage By Ecorv Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites Biochemistry V. 43 6841 2004.
ISSN: ISSN 0006-2960
PubMed: 15170321
DOI: 10.1021/BI0499056
Page generated: Tue Dec 15 03:55:39 2020

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