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Magnesium in PDB 1v14: Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)

Enzymatic activity of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)

All present enzymatic activity of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A):
3.1.21.1;

Protein crystallography data

The structure of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A), PDB code: 1v14 was solved by M.J.Mate, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.54 / 2.9
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 92.946, 124.442, 111.227, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 30.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) (pdb code 1v14). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A), PDB code: 1v14:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1v14

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1134

b:98.4
occ:1.00
 OP1 E:DC6 2.0 58.9 1.0
ND1 A:HIS102 2.9 52.6 1.0
CE1 A:HIS102 3.1 53.4 1.0
P E:DC6 3.3 58.8 1.0
NE2 A:HIS127 3.3 60.7 1.0
C4' E:DT5 3.5 59.8 1.0
O3' E:DT5 3.6 58.4 1.0
C3' E:DT5 3.8 59.7 1.0
C5' E:DT5 4.1 60.2 1.0
O5' E:DC6 4.1 57.5 1.0
ND1 A:HIS131 4.1 63.2 1.0
O5' E:DT5 4.1 61.2 1.0
CD2 A:HIS127 4.1 60.5 1.0
CG A:HIS102 4.2 53.0 1.0
CE1 A:HIS127 4.3 60.5 1.0
NE2 A:HIS102 4.4 53.9 1.0
OP2 E:DC6 4.4 58.7 1.0
CE1 A:HIS131 4.6 63.6 1.0
O A:ALA103 4.7 52.4 1.0
O A:HOH2004 4.7 56.0 1.0
O4' E:DT5 4.7 59.3 1.0
CD2 A:HIS102 5.0 53.2 1.0

Magnesium binding site 2 out of 6 in 1v14

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1134

b:70.5
occ:1.00
 OP1 I:DC6 1.9 60.1 1.0
NE2 C:HIS127 2.2 60.2 1.0
O5' I:DC6 2.3 58.3 1.0
P I:DC6 2.3 58.9 1.0
O3' I:DT5 2.6 59.0 1.0
ND1 C:HIS102 2.6 56.3 1.0
CE1 C:HIS127 3.1 59.9 1.0
CD2 C:HIS127 3.1 59.5 1.0
O C:HOH2006 3.2 44.4 1.0
CE1 C:HIS102 3.3 56.1 1.0
C5' I:DC6 3.7 56.3 1.0
CG C:HIS102 3.7 55.1 1.0
C3' I:DT5 3.8 61.2 1.0
OP2 I:DC6 3.8 57.7 1.0
CA C:HIS102 4.0 54.4 1.0
ND1 C:HIS127 4.1 59.6 1.0
C4' I:DC6 4.2 54.9 1.0
CB C:HIS102 4.2 54.5 1.0
CG C:HIS127 4.2 58.3 1.0
N C:ALA103 4.2 55.1 1.0
C4' I:DT5 4.2 62.3 1.0
O4' I:DC6 4.3 54.7 1.0
NE2 C:HIS102 4.5 55.8 1.0
C C:HIS102 4.6 54.8 1.0
CD2 C:HIS102 4.7 54.9 1.0
O C:HOH2004 4.9 34.3 1.0
O4' I:DT5 4.9 63.0 1.0
C2' I:DT5 5.0 62.0 1.0

Magnesium binding site 3 out of 6 in 1v14

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1009

b:56.1
occ:1.00
 N7 E:DG3 2.9 60.9 1.0
O6 E:DG3 3.7 61.0 1.0
C5 E:DG3 3.8 61.1 1.0
C8 E:DG3 3.8 60.8 1.0
C6 E:DG3 4.1 61.1 1.0
N6 E:DA4 4.7 62.4 1.0

Magnesium binding site 4 out of 6 in 1v14

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1009

b:56.2
occ:1.00
 N7 G:DG3 2.5 56.4 1.0
O6 G:DG3 3.2 56.9 1.0
C5 G:DG3 3.4 56.6 1.0
C8 G:DG3 3.6 56.7 1.0
C6 G:DG3 3.7 57.0 1.0
C4 G:DG3 4.7 56.8 1.0
N6 G:DA4 4.8 56.1 1.0
N9 G:DG3 4.8 56.6 1.0

Magnesium binding site 5 out of 6 in 1v14

Go back to Magnesium Binding Sites List in 1v14
Magnesium binding site 5 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1009

b:76.3
occ:1.00
 N7 I:DG3 2.7 59.0 1.0
O6 I:DG3 3.6 58.4 1.0
C5 I:DG3 3.7 58.7 1.0
C8 I:DG3 3.7 58.9 1.0
C6 I:DG3 4.0 58.9 1.0
C4 I:DG3 4.9 58.7 1.0
N9 I:DG3 4.9 58.9 1.0
N6 I:DA4 4.9 50.5 1.0

Magnesium binding site 6 out of 6 in 1v14

Go back to Magnesium Binding Sites List in 1v14
Magnesium binding site 6 out of 6 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Mg+2 and Dsdna (Resolution 2.9A) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1009

b:55.2
occ:1.00
 N7 K:DG3 2.7 56.4 1.0
C8 K:DG3 3.6 56.6 1.0
C5 K:DG3 3.7 56.5 1.0
O6 K:DG3 3.8 56.1 1.0
C6 K:DG3 4.1 56.7 1.0
N9 K:DG3 4.8 56.9 1.0
C4 K:DG3 4.9 56.1 1.0

Reference:

M.J.Mate, C.Kleanthous. Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases J.Biol.Chem. V. 279 34763 2004.
ISSN: ISSN 0021-9258
PubMed: 15190054
DOI: 10.1074/JBC.M403719200
Page generated: Sun Aug 10 05:12:20 2025

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