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Magnesium in PDB 7kiu: Structure of Recombinant Human DNASE1L3 in Complex with MG2+

Protein crystallography data

The structure of Structure of Recombinant Human DNASE1L3 in Complex with MG2+, PDB code: 7kiu was solved by J.J.Mccord, P.A.Keyel, R.B.Sutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.06 / 2.22
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.313, 72.671, 73.169, 85.39, 80.56, 88.39
R / Rfree (%) 19.1 / 23

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+ (pdb code 7kiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+, PDB code: 7kiu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7kiu

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Magnesium binding site 1 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:20.1
occ:0.90
 O A:HOH402 2.1 41.0 1.0
O A:HOH417 2.1 38.9 1.0
OD2 A:ASP222 2.2 54.2 1.0
O A:LYS226 2.2 52.0 1.0
O A:THR224 2.2 44.6 1.0
O A:THR229 2.2 49.4 1.0
OG1 A:THR224 2.6 46.3 1.0
CG A:ASP222 2.9 52.4 1.0
OD1 A:ASP222 3.0 50.1 1.0
C A:THR224 3.2 43.9 1.0
C A:LYS226 3.3 54.6 1.0
C A:THR229 3.5 50.6 1.0
CB A:THR224 3.7 44.8 1.0
CA A:THR224 3.8 42.4 1.0
C A:VAL225 4.0 50.1 1.0
O A:VAL225 4.1 51.1 1.0
N A:LYS227 4.2 59.2 1.0
N A:LYS226 4.2 52.1 1.0
OG1 A:THR229 4.2 55.1 1.0
N A:VAL225 4.2 45.0 1.0
CA A:LYS227 4.2 60.0 1.0
N A:THR224 4.2 39.9 1.0
N A:THR229 4.3 56.4 1.0
OD1 A:ASN230 4.3 65.6 1.0
CA A:LYS226 4.3 55.5 1.0
CA A:THR229 4.4 63.8 1.0
C A:LYS227 4.4 58.2 1.0
N A:ASN230 4.4 49.6 1.0
CB A:ASP222 4.4 43.4 1.0
O A:LYS227 4.5 61.4 1.0
CA A:VAL225 4.6 47.0 1.0
CA A:ASN230 4.6 49.3 1.0
CG2 A:THR224 4.8 54.1 1.0
CB A:THR229 4.9 60.6 1.0
CG A:ASN230 4.9 58.1 1.0
CB A:LYS226 5.0 57.5 1.0
N A:SER228 5.0 60.5 1.0

Magnesium binding site 2 out of 12 in 7kiu

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Magnesium binding site 2 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:85.7
occ:0.65
 O A:HOH431 1.9 30.0 0.7
O A:HOH403 2.1 62.3 1.0
O A:HOH421 2.1 30.0 0.7
OE2 A:GLU59 2.4 71.5 1.0
O A:HOH401 3.3 30.0 0.5
CD A:GLU59 3.3 75.8 1.0
O A:HOH406 3.4 30.0 0.7
OE1 A:GLU59 3.5 78.8 1.0
MG A:MG303 3.9 60.0 0.9
OD2 A:ASP273 4.4 82.5 1.0
CG A:GLU59 4.7 64.8 1.0
O A:HOH442 4.8 60.0 1.0

Magnesium binding site 3 out of 12 in 7kiu

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Magnesium binding site 3 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:60.0
occ:0.95
 O A:HOH406 2.4 30.0 0.7
ND2 A:ASN191 3.3 57.0 1.0
O A:HOH421 3.4 30.0 0.7
OD2 A:ASP189 3.5 77.4 1.0
OD1 A:ASN191 3.8 48.9 1.0
MG A:MG302 3.9 85.7 0.7
O A:HOH431 3.9 30.0 0.7
CG A:ASN191 4.0 47.5 1.0
NE2 A:HIS274 4.2 78.9 1.0
O A:HOH442 4.2 60.0 1.0
CG A:PRO158 4.3 53.3 1.0
NE2 A:HIS155 4.3 68.3 1.0
CG A:ASP189 4.5 63.3 1.0
OE2 A:GLU59 4.8 71.5 1.0
CE1 A:HIS274 4.8 68.5 1.0
OD1 A:ASP189 4.8 49.6 1.0
CD A:PRO158 5.0 47.8 1.0

Magnesium binding site 4 out of 12 in 7kiu

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Magnesium binding site 4 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:40.5
occ:1.00
 O B:THR229 2.1 59.3 1.0
O B:HOH411 2.1 52.4 1.0
O B:LYS226 2.2 58.2 1.0
OD2 B:ASP222 2.2 53.2 1.0
O B:THR224 2.4 48.3 1.0
OG1 B:THR224 2.5 58.0 1.0
OD1 B:ASP222 2.8 54.2 1.0
CG B:ASP222 2.8 49.3 1.0
C B:THR229 3.3 58.9 1.0
C B:THR224 3.3 47.6 1.0
C B:LYS226 3.3 76.2 1.0
CB B:THR224 3.7 44.8 1.0
CA B:THR224 3.9 43.1 1.0
OG1 B:THR229 4.1 83.8 1.0
N B:LYS227 4.2 77.3 1.0
CA B:LYS227 4.2 83.5 1.0
N B:THR229 4.2 61.7 1.0
C B:VAL225 4.2 53.7 1.0
N B:ASN230 4.2 55.5 1.0
CA B:THR229 4.2 73.4 1.0
N B:THR224 4.3 41.4 1.0
O B:VAL225 4.3 64.2 1.0
N B:LYS226 4.3 55.2 1.0
C B:LYS227 4.3 75.8 1.0
CB B:ASP222 4.3 49.2 1.0
CA B:ASN230 4.3 63.3 1.0
N B:VAL225 4.3 51.2 1.0
CA B:LYS226 4.4 63.5 1.0
O B:LYS227 4.4 81.4 1.0
CA B:VAL225 4.8 54.0 1.0
CG B:ASN230 4.8 81.7 1.0
CB B:THR229 4.8 63.2 1.0
CG2 B:THR224 4.8 50.2 1.0
OD1 B:ASN230 4.8 86.7 1.0
ND2 B:ASN230 4.9 84.0 1.0
N B:SER228 4.9 72.5 1.0
CB B:LYS226 4.9 63.5 1.0

Magnesium binding site 5 out of 12 in 7kiu

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Magnesium binding site 5 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:60.6
occ:1.00
 O B:HOH403 2.1 30.0 0.5
O B:HOH434 2.2 30.0 0.7
O B:HOH432 2.5 30.0 0.6
OE2 B:GLU59 2.5 66.0 1.0
O B:HOH404 2.6 67.5 1.0
OD2 B:ASP273 3.0 80.7 1.0
O B:HOH431 3.4 30.0 0.5
OD1 B:ASP273 3.4 78.0 1.0
CD B:GLU59 3.4 72.1 1.0
CG B:ASP273 3.6 75.1 1.0
CE1 B:HIS274 3.7 71.7 1.0
OE1 B:GLU59 3.7 75.2 1.0
ND1 B:HIS274 4.0 71.3 1.0
OD1 B:ASN27 4.0 59.0 1.0
CD B:ARG29 4.3 65.8 1.0
CG B:ARG29 4.3 58.8 1.0
ND2 B:ASN27 4.3 55.3 1.0
MG B:MG303 4.4 50.0 0.8
CG B:ASN27 4.5 54.8 1.0
CB B:ARG29 4.6 55.0 1.0
CA B:ARG29 4.8 57.0 1.0
CG B:GLU59 4.8 59.3 1.0
NE2 B:HIS274 4.9 82.5 1.0

Magnesium binding site 6 out of 12 in 7kiu

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Magnesium binding site 6 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:50.0
occ:0.85
 O B:HOH431 2.5 30.0 0.5
O B:HOH432 2.7 30.0 0.6
O B:HOH434 2.8 30.0 0.7
O B:HOH435 3.0 68.2 1.0
O B:HOH404 3.6 67.5 1.0
OD1 B:ASN191 3.7 56.3 1.0
OG A:SER195 3.9 78.2 1.0
CB A:SER195 4.0 82.2 1.0
CG B:PRO158 4.1 71.3 1.0
MG B:MG302 4.4 60.6 1.0
CG B:ASN191 4.5 60.7 1.0
ND2 B:ASN191 4.7 45.2 1.0
CE1 B:HIS274 4.8 71.7 1.0
OD2 B:ASP189 4.8 62.7 1.0
CD B:PRO158 5.0 53.9 1.0

Magnesium binding site 7 out of 12 in 7kiu

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Magnesium binding site 7 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:29.2
occ:1.00
 OD2 C:ASP222 2.1 42.6 1.0
O C:LYS226 2.2 47.1 1.0
O C:HOH417 2.2 41.4 1.0
O C:THR229 2.2 51.4 1.0
O C:THR224 2.3 42.5 1.0
O C:HOH416 2.4 51.0 1.0
OG1 C:THR224 2.6 54.3 1.0
CG C:ASP222 2.8 48.9 1.0
OD1 C:ASP222 2.9 61.7 1.0
C C:THR224 3.3 43.0 1.0
C C:LYS226 3.3 49.0 1.0
C C:THR229 3.4 49.8 1.0
CB C:THR224 3.8 44.8 1.0
CA C:THR224 3.9 46.3 1.0
C C:VAL225 4.1 46.7 1.0
CA C:LYS227 4.1 66.6 1.0
O C:VAL225 4.1 49.6 1.0
N C:LYS227 4.1 53.8 1.0
N C:LYS226 4.2 52.1 1.0
N C:THR224 4.2 39.5 1.0
OG1 C:THR229 4.2 69.2 1.0
N C:VAL225 4.3 47.5 1.0
CB C:ASP222 4.3 43.0 1.0
OD1 C:ASN230 4.3 70.5 1.0
N C:THR229 4.3 49.3 1.0
CA C:LYS226 4.4 53.9 1.0
N C:ASN230 4.4 61.5 1.0
CA C:THR229 4.4 54.1 1.0
C C:LYS227 4.4 63.5 1.0
CA C:ASN230 4.5 57.8 1.0
O C:LYS227 4.6 69.2 1.0
CA C:VAL225 4.7 45.5 1.0
NZ C:LYS227 4.8 52.4 1.0
CG C:ASN230 4.9 75.4 1.0
CG2 C:THR224 4.9 44.8 1.0
CB C:THR229 4.9 55.8 1.0
CB C:LYS226 5.0 49.9 1.0

Magnesium binding site 8 out of 12 in 7kiu

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Magnesium binding site 8 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:72.0
occ:1.00
 O C:HOH403 1.9 30.0 0.7
O C:HOH408 2.1 65.1 1.0
O C:HOH404 2.1 72.5 1.0
O C:HOH402 2.2 30.0 0.5
O C:HOH407 2.2 30.0 0.5
OE2 C:GLU59 2.3 78.7 1.0
CD C:GLU59 3.3 75.0 1.0
OE1 C:GLU59 3.5 78.7 1.0
MG C:MG303 3.8 79.0 1.0
O C:HOH440 4.1 87.8 0.9
OD2 C:ASP273 4.1 91.8 1.0
O C:HOH421 4.3 63.0 1.0
OD1 C:ASP273 4.7 86.0 1.0
CG C:GLU59 4.7 71.5 1.0
ND2 C:ASN27 4.8 58.0 1.0
CG C:ASP273 4.8 85.1 1.0
CG C:ARG29 4.9 64.0 1.0
NE2 C:HIS155 4.9 66.2 1.0
OD1 C:ASN27 4.9 63.6 1.0
CD C:ARG29 4.9 63.7 1.0
CE1 C:HIS155 5.0 61.1 1.0

Magnesium binding site 9 out of 12 in 7kiu

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Magnesium binding site 9 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:79.0
occ:0.98
 O C:HOH407 2.3 30.0 0.5
O C:HOH440 2.3 87.8 0.9
OD2 C:ASP189 2.8 72.8 1.0
NE2 C:HIS274 3.1 76.2 1.0
O C:HOH421 3.3 63.0 1.0
OD1 C:ASN191 3.3 65.1 1.0
O C:HOH403 3.4 30.0 0.7
CE1 C:HIS274 3.6 66.6 1.0
CG C:ASP189 3.8 63.1 1.0
MG C:MG302 3.8 72.0 1.0
OD1 C:ASP189 4.1 53.7 1.0
CG C:ASN191 4.1 52.7 1.0
ND2 C:ASN191 4.2 49.8 1.0
CD2 C:HIS274 4.2 64.8 1.0
NE2 C:HIS155 4.4 66.2 1.0
O C:HOH402 4.5 30.0 0.5
ND2 C:ASN27 4.5 58.0 1.0
O C:HOH408 4.6 65.1 1.0
OE2 C:GLU59 4.7 78.7 1.0
ND1 C:HIS274 4.8 60.6 1.0

Magnesium binding site 10 out of 12 in 7kiu

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Magnesium binding site 10 out of 12 in the Structure of Recombinant Human DNASE1L3 in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Recombinant Human DNASE1L3 in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.8
occ:1.00
 O D:LYS226 2.1 53.0 1.0
O D:THR229 2.1 54.2 1.0
OD2 D:ASP222 2.2 53.3 1.0
O D:THR224 2.2 49.3 1.0
O D:HOH417 2.3 47.0 1.0
O D:HOH411 2.3 41.3 1.0
OG1 D:THR224 2.5 47.2 1.0
CG D:ASP222 2.9 52.8 1.0
OD1 D:ASP222 2.9 48.0 1.0
C D:THR224 3.2 43.0 1.0
C D:LYS226 3.3 54.9 1.0
C D:THR229 3.4 63.8 1.0
CB D:THR224 3.6 41.2 1.0
CA D:THR224 3.8 35.5 1.0
C D:VAL225 4.1 40.9 1.0
OG1 D:THR229 4.1 54.0 1.0
O D:VAL225 4.1 51.6 1.0
N D:LYS226 4.2 41.3 1.0
N D:THR224 4.2 34.8 1.0
N D:LYS227 4.2 54.2 1.0
N D:VAL225 4.2 44.2 1.0
N D:THR229 4.3 66.8 1.0
CA D:LYS226 4.3 45.0 1.0
CA D:THR229 4.3 69.2 1.0
N D:ASN230 4.3 55.8 1.0
CA D:LYS227 4.3 69.7 1.0
OD1 D:ASN230 4.3 83.9 1.0
CB D:ASP222 4.4 45.9 1.0
C D:LYS227 4.5 72.1 1.0
CA D:ASN230 4.5 63.4 1.0
O D:LYS227 4.6 81.3 1.0
CA D:VAL225 4.6 40.2 1.0
CG2 D:THR224 4.7 53.5 1.0
CB D:THR229 4.8 73.1 1.0
CB D:LYS226 4.9 55.8 1.0
CG D:ASN230 4.9 78.8 1.0

Reference:

J.J.Mccord, P.A.Keyel, R.B.Sutton. Crystal Structure of DNASE1L3 Demonstrating Two Divalent Cation Catalytic Mechanism To Be Published.
Page generated: Wed Oct 2 22:19:58 2024

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