Magnesium in PDB 4m30: Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage)

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

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

Protein crystallography data

The structure of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage), PDB code: 4m30 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) 29.12 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.104, 81.104, 223.962, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage) (pdb code 4m30). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage), PDB code: 4m30:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4m30

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Magnesium binding site 1 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:60.5
occ:1.00
 OE2 A:GLU110 2.0 62.5 1.0
OD1 A:ASP44 2.0 58.6 1.0
O D:HOH201 2.0 66.7 1.0
OP1 C:A103 2.1 67.7 1.0
O3' D:U28 2.1 62.2 1.0
O A:HOH601 2.1 62.1 1.0
CG A:ASP44 3.0 65.9 1.0
CD A:GLU110 3.1 64.0 1.0
C3' D:U28 3.4 59.1 1.0
CB A:ASP44 3.4 63.2 1.0
O2' D:U28 3.5 63.6 1.0
P C:A103 3.5 71.9 1.0
MG A:MG502 3.5 69.7 1.0
OE1 A:GLU110 3.6 69.2 1.0
C2' D:U28 4.0 58.8 1.0
C4' D:U28 4.0 65.5 1.0
CA A:ASP44 4.0 60.8 1.0
O5' C:A103 4.0 58.5 1.0
OD2 A:ASP44 4.1 61.7 1.0
OP3 C:A103 4.2 66.1 1.0
C5' C:A103 4.3 62.7 1.0
O A:HOH602 4.3 69.5 1.0
CG A:GLU110 4.4 61.0 1.0
OD1 A:ASN48 4.5 59.1 1.0
O A:ILE75 4.5 62.4 1.0
O A:HOH603 4.5 68.8 1.0
CE2 A:PHE80 4.5 64.5 1.0
OP2 C:A103 4.6 78.9 1.0
C5' D:U28 4.7 58.4 1.0
C A:ASP44 4.9 63.2 1.0
ND2 A:ASN48 4.9 55.9 1.0
O A:ASP44 4.9 60.8 1.0

Magnesium binding site 2 out of 9 in 4m30

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Magnesium binding site 2 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:69.7
occ:1.00
 O A:HOH602 2.0 69.5 1.0
O A:HOH603 2.0 68.8 1.0
OE2 A:GLU40 2.0 73.8 1.0
OE1 A:GLU110 2.1 69.2 1.0
OP2 C:A103 2.1 78.9 1.0
OP1 C:A103 2.1 67.7 1.0
P C:A103 2.4 71.9 1.0
CD A:GLU110 3.1 64.0 1.0
CD A:GLU40 3.2 71.7 1.0
OE2 A:GLU110 3.3 62.5 1.0
OP3 C:A103 3.5 66.1 1.0
MG A:MG501 3.5 60.5 1.0
O5' C:A103 3.6 58.5 1.0
CG A:GLU40 3.7 61.6 1.0
O A:HOH622 3.9 77.5 1.0
C5' C:A103 3.9 62.7 1.0
O D:HOH201 4.0 66.7 1.0
CB A:ASP44 4.2 63.2 1.0
OE1 A:GLU40 4.3 71.2 1.0
OD1 A:ASP107 4.3 74.7 1.0
O A:GLU40 4.3 62.8 1.0
O3' D:U28 4.4 62.2 1.0
CG A:GLU110 4.4 61.0 1.0
OD1 A:ASP44 4.5 58.6 1.0
CG A:ASP44 4.7 65.9 1.0
CB A:GLU110 4.8 61.5 1.0
C A:GLU40 4.9 59.2 1.0
CB A:GLU40 4.9 61.8 1.0

Magnesium binding site 3 out of 9 in 4m30

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Magnesium binding site 3 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:60.1
occ:1.00
 OD1 B:ASP44 1.9 52.3 1.0
O C:HOH218 2.0 58.4 1.0
OP1 D:A104 2.0 72.1 1.0
OE2 B:GLU110 2.1 64.9 1.0
O3' C:U28 2.1 64.3 1.0
O B:HOH401 2.1 55.9 1.0
CG B:ASP44 3.0 61.9 1.0
CD B:GLU110 3.1 70.2 1.0
C3' C:U28 3.4 49.0 1.0
P D:A104 3.4 69.3 1.0
OE1 B:GLU110 3.5 69.7 1.0
CB B:ASP44 3.5 59.6 1.0
O2' C:U28 3.6 51.5 1.0
MG B:MG302 3.6 75.8 1.0
OD2 B:ASP44 4.0 61.5 1.0
C2' C:U28 4.0 57.9 1.0
C4' C:U28 4.0 52.9 1.0
O5' D:A104 4.0 63.6 1.0
OP3 D:A104 4.0 64.5 1.0
CA B:ASP44 4.3 62.1 1.0
C5' D:A104 4.4 63.2 1.0
O B:HOH414 4.4 66.6 1.0
CG B:GLU110 4.5 67.1 1.0
O B:ILE75 4.5 59.4 1.0
CE2 B:PHE80 4.5 68.6 1.0
OD1 B:ASN48 4.5 60.4 1.0
OP2 D:A104 4.6 82.2 1.0
C5' C:U28 4.7 53.9 1.0
ND2 B:ASN48 4.8 54.9 1.0

Magnesium binding site 4 out of 9 in 4m30

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Magnesium binding site 4 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:75.8
occ:1.00
 O B:HOH414 2.0 66.6 1.0
OE1 B:GLU110 2.1 69.7 1.0
OE2 B:GLU40 2.1 84.1 1.0
OP2 D:A104 2.1 82.2 1.0
OP1 D:A104 2.2 72.1 1.0
P D:A104 2.5 69.3 1.0
CD B:GLU110 3.1 70.2 1.0
CD B:GLU40 3.3 82.7 1.0
OP3 D:A104 3.4 64.5 1.0
O D:HOH211 3.5 76.8 1.0
OE2 B:GLU110 3.5 64.9 1.0
MG B:MG301 3.6 60.1 1.0
O D:HOH212 3.8 80.1 1.0
CG B:GLU40 3.8 74.9 1.0
O5' D:A104 3.9 63.6 1.0
OD1 B:ASP107 4.1 79.2 1.0
O C:HOH218 4.1 58.4 1.0
C5' D:A104 4.3 63.2 1.0
OE1 B:GLU40 4.3 80.5 1.0
CG B:GLU110 4.4 67.1 1.0
O3' C:U28 4.5 64.3 1.0
CB B:ASP44 4.6 59.6 1.0
OD1 B:ASP44 4.7 52.3 1.0
CG B:ASP107 4.7 80.9 1.0
O B:GLU40 4.8 70.5 1.0
OE2 A:GLU64 4.9 96.0 1.0
CG B:ASP44 4.9 61.9 1.0

Magnesium binding site 5 out of 9 in 4m30

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Magnesium binding site 5 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:90.9
occ:1.00
 OP1 C:A2 2.0 80.0 1.0
O A:HOH623 2.0 84.4 1.0
O A:HOH621 2.0 74.5 1.0
O C:HOH215 2.0 84.9 1.0
O A:HOH622 2.1 77.5 1.0
O C:HOH216 2.1 81.4 1.0
P C:A2 3.4 83.8 1.0
OE2 B:GLU64 3.9 85.7 1.0
OD2 A:ASP107 4.0 73.2 1.0
C5' C:A2 4.1 72.4 1.0
OP2 C:A2 4.1 79.7 1.0
OD1 A:ASP107 4.3 74.7 1.0
O5' C:A2 4.3 80.0 1.0
OE1 A:GLU40 4.3 71.2 1.0
OP3 C:A2 4.3 77.7 1.0
CG A:ASP107 4.5 73.4 1.0
OE2 A:GLU40 4.6 73.8 1.0
OP2 C:A103 4.7 78.9 1.0
OP1 C:U19 4.8 79.3 1.0
CD A:GLU40 4.9 71.7 1.0
O C:HOH213 4.9 86.8 1.0
CD B:GLU64 4.9 0.9 1.0

Magnesium binding site 6 out of 9 in 4m30

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Magnesium binding site 6 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (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 Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:83.7
occ:1.00
 OP2 C:A3 2.0 64.7 1.0
OP2 C:A2 2.0 79.7 1.0
O C:HOH213 2.0 86.8 1.0
O C:HOH217 2.1 76.2 1.0
O C:HOH214 2.1 76.8 1.0
P C:A2 3.3 83.8 1.0
P C:A3 3.5 74.5 1.0
O5' C:A2 3.7 80.0 1.0
O C:HOH216 4.1 81.4 1.0
C3' C:A2 4.1 74.6 1.0
N7 C:A3 4.2 60.1 1.0
OP1 C:A2 4.2 80.0 1.0
O5' C:A3 4.3 66.1 1.0
O3' C:A2 4.3 85.7 1.0
OP3 C:A2 4.3 77.7 1.0
C8 C:A3 4.4 63.9 1.0
C5' C:A2 4.4 72.4 1.0
OP1 C:A3 4.4 89.7 1.0
O C:HOH202 4.7 68.1 1.0
C4' C:A2 4.9 72.1 1.0

Magnesium binding site 7 out of 9 in 4m30

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Magnesium binding site 7 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:95.9
occ:1.00
 O D:HOH209 2.0 82.6 1.0
O D:HOH211 2.0 76.8 1.0
OP1 D:A2 2.0 85.2 1.0
O A:HOH624 2.0 82.3 1.0
O B:HOH415 2.1 80.4 1.0
O D:HOH212 2.1 80.1 1.0
P D:A2 3.2 84.0 1.0
OE1 A:GLU64 3.5 86.8 1.0
C5' D:A2 3.8 72.8 1.0
OP2 D:A2 3.8 82.7 1.0
OE2 A:GLU64 3.9 96.0 1.0
OD2 B:ASP107 3.9 83.9 1.0
O5' D:A2 3.9 71.7 1.0
CD A:GLU64 4.1 0.1 1.0
OE2 B:GLU40 4.1 84.1 1.0
OE1 B:GLU40 4.2 80.5 1.0
OP2 D:A104 4.2 82.2 1.0
OP3 D:A2 4.4 77.5 1.0
CD B:GLU40 4.6 82.7 1.0
CG B:ASP107 4.7 80.9 1.0
OP1 D:U19 4.7 96.9 1.0
OD1 B:ASP107 4.7 79.2 1.0

Magnesium binding site 8 out of 9 in 4m30

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Magnesium binding site 8 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:83.1
occ:1.00
 O D:HOH204 2.0 81.7 1.0
OP2 D:A3 2.0 55.8 1.0
OP2 D:A2 2.1 82.7 1.0
O D:HOH210 2.1 69.5 1.0
P D:A3 3.5 70.4 1.0
P D:A2 3.6 84.0 1.0
OP3 D:A2 4.1 77.5 1.0
O A:HOH624 4.1 82.3 1.0
C3' D:A2 4.2 70.2 1.0
O5' D:A3 4.3 67.4 1.0
O5' D:A2 4.3 71.7 1.0
N7 D:A3 4.3 59.3 1.0
O3' D:A2 4.4 83.8 1.0
OP1 D:A3 4.5 79.0 1.0
C8 D:A3 4.5 60.9 1.0
OP1 D:A2 4.6 85.2 1.0
C5' D:A2 4.8 72.8 1.0
O D:HOH208 4.8 71.2 1.0

Magnesium binding site 9 out of 9 in 4m30

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Magnesium binding site 9 out of 9 in the Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Rnase III Complexed with Double-Stranded Rna and Amp (Type II Cleavage) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg103

b:92.0
occ:1.00
 OP1 D:C23 3.1 84.0 1.0
OP2 D:C23 3.6 80.3 1.0
P D:C23 3.8 87.8 1.0
CD B:LYS202 4.3 89.5 1.0
OE2 B:GLU206 4.6 74.6 1.0
CB B:LYS202 4.6 82.3 1.0
O5' D:C23 4.7 80.9 1.0
OE1 B:GLU206 5.0 77.1 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 Dec 14 19:11:28 2020

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