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Magnesium in PDB 4m2z: Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)

Enzymatic activity of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)

All present enzymatic activity of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage):
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage), PDB code: 4m2z was solved by J.Gan, Y.-H.Liang, G.X.Shaw, J.E.Tropea, D.S.Waugh, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.11 / 2.85
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.131, 81.131, 223.892, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 28.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) (pdb code 4m2z). 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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage), PDB code: 4m2z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4m2z

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Magnesium binding site 1 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:0.8
occ:1.00
 OP1 C:C103 2.0 0.7 1.0
O A:HOH601 2.0 84.1 1.0
OD2 A:ASP44 2.0 99.0 1.0
O D:HOH205 2.0 95.1 1.0
OE1 A:GLU110 2.1 91.5 1.0
O3' D:G28 2.1 0.3 1.0
CD A:GLU110 2.9 0.4 1.0
OE2 A:GLU110 2.9 0.6 1.0
CG A:ASP44 3.1 96.1 1.0
P C:C103 3.5 0.4 1.0
C3' D:G28 3.5 94.7 1.0
CB A:ASP44 3.7 89.4 1.0
O2' D:G28 4.0 98.5 1.0
OP3 C:C103 4.0 96.8 1.0
OD1 A:ASP44 4.1 0.4 1.0
C4' D:G28 4.2 97.4 1.0
C5' C:C103 4.2 98.9 1.0
C2' D:G28 4.3 94.8 1.0
O5' C:C103 4.3 98.9 1.0
CA A:ASP44 4.3 85.8 1.0
CG A:GLU110 4.4 97.0 1.0
OP2 C:C103 4.4 0.8 1.0
CE2 A:PHE80 4.4 0.1 1.0
OE2 A:GLU40 4.5 1.0 1.0
O A:ILE75 4.7 98.3 1.0
C5' D:G28 4.8 93.2 1.0
OD1 A:ASN48 4.8 92.2 1.0
CB A:GLU110 4.9 95.7 1.0
CD2 A:PHE80 4.9 92.3 1.0

Magnesium binding site 2 out of 6 in 4m2z

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Magnesium binding site 2 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:0.2
occ:1.00
 OP1 D:C103 2.0 0.5 1.0
OD2 B:ASP44 2.0 0.2 1.0
O D:HOH206 2.0 0.4 1.0
O B:HOH402 2.0 83.8 1.0
OE2 B:GLU110 2.0 0.7 1.0
O3' C:G28 2.0 0.2 1.0
CG B:ASP44 2.4 0.2 1.0
OD1 B:ASP44 2.6 0.8 1.0
CD B:GLU110 3.1 0.8 1.0
C3' C:G28 3.4 90.9 1.0
P D:C103 3.4 0.3 1.0
OE1 B:GLU110 3.5 0.6 1.0
CB B:ASP44 3.5 0.1 1.0
O2' C:G28 3.7 94.9 1.0
C5' D:C103 3.8 0.6 1.0
O5' D:C103 4.0 0.6 1.0
C2' C:G28 4.1 89.2 1.0
OP3 D:C103 4.1 0.8 1.0
C4' C:G28 4.2 91.6 1.0
CG B:GLU110 4.4 0.0 1.0
OE2 B:GLU40 4.4 0.6 1.0
OP2 D:C103 4.5 0.9 1.0
CA B:ASP44 4.5 0.8 1.0
ND2 B:ASN48 4.5 99.9 1.0
CE2 B:PHE80 4.8 94.9 1.0
C5' C:G28 4.9 91.5 1.0
C4' D:C103 4.9 98.8 1.0

Magnesium binding site 3 out of 6 in 4m2z

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Magnesium binding site 3 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:0.2
occ:1.00
 OP1 C:A2 2.0 0.0 1.0
O C:HOH205 2.0 0.2 1.0
O A:HOH606 2.1 0.7 1.0
O C:HOH204 2.1 0.8 1.0
P C:A2 3.2 0.3 1.0
OP2 C:A2 3.6 0.7 1.0
OE1 B:GLU64 3.6 0.4 1.0
OE1 A:GLU40 3.8 0.1 1.0
C5' C:A2 4.0 0.2 1.0
O5' C:A2 4.1 0.9 1.0
OE2 B:GLU64 4.2 0.6 1.0
CD B:GLU64 4.2 0.9 1.0
OP3 C:A2 4.2 0.2 1.0
MG C:MG102 4.7 0.8 1.0
OP2 C:C103 4.7 0.8 1.0
OD2 A:ASP107 4.9 0.8 1.0
OP2 C:A3 4.9 0.8 1.0

Magnesium binding site 4 out of 6 in 4m2z

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Magnesium binding site 4 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:0.8
occ:1.00
 OP2 C:A3 2.0 0.8 1.0
OP2 C:A2 2.0 0.7 1.0
P C:A3 3.5 0.7 1.0
P C:A2 3.5 0.3 1.0
O C:HOH205 3.5 0.2 1.0
OP3 C:A2 4.2 0.2 1.0
O5' C:A3 4.2 0.1 1.0
O5' C:A2 4.3 0.9 1.0
OP1 C:A3 4.3 0.9 1.0
OP1 C:A2 4.4 0.0 1.0
O3' C:A2 4.4 0.4 1.0
C3' C:A2 4.4 0.7 1.0
N7 C:A3 4.5 0.6 1.0
C8 C:A3 4.7 0.2 1.0
MG C:MG101 4.7 0.2 1.0
C5' C:A2 4.8 0.2 1.0

Magnesium binding site 5 out of 6 in 4m2z

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Magnesium binding site 5 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:0.5
occ:1.00
 OP1 D:A2 2.0 0.3 1.0
O B:HOH403 2.0 0.1 1.0
O D:HOH207 2.0 0.2 1.0
O D:HOH208 2.0 0.8 1.0
P D:A2 3.2 0.9 1.0
OE2 A:GLU64 3.4 0.4 1.0
OE1 A:GLU64 3.6 0.6 1.0
OP2 D:A2 3.7 0.1 1.0
OP2 D:C103 3.7 0.9 1.0
OD2 B:ASP107 3.8 0.0 1.0
CD A:GLU64 3.9 0.0 1.0
OE2 B:GLU40 4.0 0.6 1.0
OE1 B:GLU40 4.0 0.6 1.0
C5' D:A2 4.1 0.4 1.0
O5' D:A2 4.1 0.7 1.0
CD B:GLU40 4.2 0.1 1.0
OP3 D:A2 4.2 0.5 1.0
CG B:ASP107 4.8 0.9 1.0

Magnesium binding site 6 out of 6 in 4m2z

Go back to Magnesium Binding Sites List in 4m2z
Magnesium binding site 6 out of 6 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage)


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 Rnase III Complexed with Double-Stranded Rna and Cmp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:0.9
occ:1.00
 OP2 D:A3 2.0 0.1 1.0
OP2 D:A2 2.0 0.1 1.0
P D:A2 3.4 0.9 1.0
P D:A3 3.5 0.1 1.0
OP3 D:A2 3.9 0.5 1.0
O5' D:A2 3.9 0.7 1.0
O D:HOH208 4.0 0.8 1.0
C3' D:A2 4.3 0.0 1.0
O3' D:A2 4.3 0.1 1.0
OP1 D:A3 4.3 0.7 1.0
O5' D:A3 4.3 0.8 1.0
OP1 D:A2 4.6 0.3 1.0
C5' D:A2 4.6 0.4 1.0
N7 D:A3 5.0 90.9 1.0

Reference:

D.L.Court, J.Gan, Y.H.Liang, G.X.Shaw, J.E.Tropea, N.Costantino, D.S.Waugh, X.Ji. Rnase III: Genetics and Function; Structure and Mechanism. Annu. Rev. Genet. V. 47 405 2013.
PubMed: 24274754
DOI: 10.1146/ANNUREV-GENET-110711-155618
Page generated: Mon Aug 19 20:14:47 2024

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