Atomistry » Magnesium » PDB 4lsh-4m34 » 4m30
Atomistry »
  Magnesium »
    PDB 4lsh-4m34 »
      4m30 »

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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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

Go back to Magnesium Binding Sites List in 4m30
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 Aug 19 20:14:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy