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Magnesium in PDB 5hmm: Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

Enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

All present enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions:
3.1.11.3;

Protein crystallography data

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hmm was solved by C.S.Flemming, S.E.Sedelnikova, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.831, 58.591, 59.729, 66.88, 79.40, 73.78
R / Rfree (%) 14.8 / 19.7

Other elements in 5hmm:

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions (pdb code 5hmm). 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 T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hmm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5hmm

Go back to Magnesium Binding Sites List in 5hmm
Magnesium binding site 1 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:10.0
occ:1.00
 O A:HOH524 2.0 10.8 1.0
O A:HOH642 2.0 11.4 1.0
O A:HOH440 2.1 10.2 1.0
O A:HOH425 2.1 12.8 1.0
O A:HOH438 2.1 11.8 1.0
OD1 A:ASP130 2.2 9.0 1.0
CG A:ASP130 3.2 9.0 1.0
OD2 A:ASP130 3.5 15.4 1.0
MG A:MG303 3.6 32.4 1.0
OD2 A:ASP153 3.9 20.9 1.0
OE2 A:GLU128 4.0 20.3 1.0
O A:HOH575 4.1 34.4 1.0
OD2 A:ASP68 4.2 10.9 1.0
OD1 A:ASP68 4.2 11.6 1.0
NE1 A:TRP156 4.3 10.5 1.0
OD2 A:ASP26 4.3 8.3 1.0
O A:HOH510 4.3 31.3 1.0
OD1 A:ASP26 4.4 11.5 1.0
N A:ASP130 4.5 7.1 1.0
CB A:ASP130 4.5 8.8 1.0
CG A:ASP68 4.6 12.9 1.0
O A:HOH608 4.7 32.2 1.0
CG A:ASP26 4.8 7.7 1.0
CA A:ASP130 4.9 8.0 1.0
CG A:ASP153 5.0 16.0 1.0

Magnesium binding site 2 out of 6 in 5hmm

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Magnesium binding site 2 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.4
occ:1.00
 O A:HOH524 1.9 10.8 1.0
OD2 A:ASP130 2.2 15.4 1.0
OD2 A:ASP153 2.4 20.9 1.0
OD2 A:ASP155 2.5 29.6 1.0
CG A:ASP130 3.3 9.0 1.0
CG A:ASP155 3.4 31.5 1.0
CG A:ASP153 3.5 16.0 1.0
O A:HOH592 3.5 33.0 1.0
O A:HOH454 3.5 30.6 1.0
MG A:MG302 3.6 10.0 1.0
OD1 A:ASP130 3.6 9.0 1.0
CB A:ASP155 3.6 26.5 1.0
O A:HOH438 3.7 11.8 1.0
O A:HOH401 3.8 44.0 1.0
OD1 A:ASP153 3.9 14.7 1.0
O A:HOH575 4.3 34.4 1.0
OE2 A:GLU128 4.3 20.3 1.0
O A:HOH642 4.5 11.4 1.0
OD1 A:ASP155 4.5 32.1 1.0
CB A:ASP130 4.5 8.8 1.0
O A:HOH425 4.6 12.8 1.0
NE1 A:TRP156 4.7 10.5 1.0
CD1 A:TRP156 4.7 10.0 1.0
O A:HOH418 4.7 38.5 1.0
CB A:ASP153 4.8 11.8 1.0
OD2 A:ASP204 4.8 34.1 1.0

Magnesium binding site 3 out of 6 in 5hmm

Go back to Magnesium Binding Sites List in 5hmm
Magnesium binding site 3 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:33.1
occ:0.70
 O A:HOH401 2.0 44.0 1.0
O A:HOH418 2.1 38.5 1.0
O A:HOH556 2.2 34.4 1.0
OD2 A:ASP201 2.3 40.1 1.0
O A:HOH532 2.5 37.8 1.0
OD1 A:ASP155 2.7 32.1 1.0
CG A:ASP201 3.3 32.8 1.0
CG A:ASP155 3.4 31.5 1.0
OD2 A:ASP155 3.5 29.6 1.0
OD1 A:ASP201 3.6 27.4 1.0
O A:HOH403 3.8 39.2 1.0
OD2 A:ASP204 4.0 34.1 1.0
O A:HOH560 4.2 38.4 1.0
OD1 A:ASP153 4.3 14.7 1.0
CB A:ASP201 4.6 22.9 1.0
CB A:ASP155 4.7 26.5 1.0
CG A:ASP204 4.8 24.9 1.0

Magnesium binding site 4 out of 6 in 5hmm

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Magnesium binding site 4 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:7.0
occ:1.00
 O B:HOH429 2.0 7.0 1.0
O B:HOH438 2.0 7.8 1.0
O B:HOH676 2.1 10.7 1.0
O B:HOH462 2.1 10.9 1.0
O B:HOH412 2.1 7.5 1.0
OD1 B:ASP130 2.2 8.2 1.0
CG B:ASP130 3.2 9.3 1.0
OD2 B:ASP130 3.5 13.2 1.0
OD2 B:ASP153 3.9 18.6 1.0
NE1 B:TRP156 4.1 9.5 1.0
O B:HOH435 4.1 32.4 1.0
OD2 B:ASP68 4.1 13.0 1.0
OE2 B:GLU128 4.2 22.2 1.0
OD1 B:ASP68 4.3 13.1 1.0
OD2 B:ASP26 4.3 7.5 1.0
OD1 B:ASP26 4.3 9.0 1.0
O B:HOH537 4.5 39.9 1.0
CB B:ASP130 4.5 8.4 1.0
N B:ASP130 4.5 7.1 1.0
NZ B:LYS83 4.6 21.1 1.0
CG B:ASP68 4.6 11.0 1.0
O B:HOH405 4.6 32.5 1.0
CG B:ASP26 4.8 6.8 1.0
O B:HOH649 4.8 18.8 1.0
CD1 B:TRP156 4.9 9.2 1.0
CA B:ASP130 5.0 8.0 1.0

Magnesium binding site 5 out of 6 in 5hmm

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Magnesium binding site 5 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:45.3
occ:1.00
 O B:HOH682 1.9 33.4 1.0
O B:HOH449 2.1 51.4 1.0
O B:HOH452 2.2 35.7 1.0
OD2 B:ASP201 2.2 26.2 1.0
O B:HOH506 2.4 49.9 1.0
O B:HOH604 2.9 45.0 1.0
CG B:ASP201 3.2 18.3 1.0
OD1 B:ASP201 3.4 15.0 1.0
O A:HOH404 3.6 31.9 1.0
OD2 B:ASP204 4.1 37.3 1.0
OD1 B:ASP155 4.3 19.7 1.0
O A:HOH489 4.3 22.7 1.0
O B:HOH573 4.4 32.5 1.0
CB B:ASP201 4.6 13.8 1.0
CE B:LYS196 4.6 15.7 0.5
CG B:ASP204 4.6 22.8 1.0
O B:HOH634 4.6 52.1 1.0
OD2 B:ASP155 4.7 33.5 1.0
OD1 B:ASP204 4.8 26.6 1.0
CG B:ASP155 4.9 22.0 1.0
O B:HOH571 4.9 16.8 1.0

Magnesium binding site 6 out of 6 in 5hmm

Go back to Magnesium Binding Sites List in 5hmm
Magnesium binding site 6 out of 6 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:19.1
occ:1.00
 O B:HOH600 2.0 20.2 1.0
O B:HOH401 2.0 22.8 1.0
O B:HOH443 2.1 19.4 1.0
O B:HOH594 2.1 20.5 1.0
O B:HOH418 2.1 22.5 1.0
OD1 B:ASP87 2.2 15.1 1.0
CG B:ASP87 3.2 16.7 1.0
OD2 B:ASP87 3.5 17.4 1.0
OE1 B:GLU88 4.1 27.2 1.0
OD1 B:ASN85 4.1 18.9 1.0
O B:HOH723 4.2 29.7 1.0
N B:GLU88 4.4 12.7 1.0
CB B:ASP87 4.5 13.9 1.0
OE2 B:GLU81 4.5 41.4 1.0
N B:ASP87 4.5 14.1 1.0
O B:HOH408 4.6 7.3 1.0
OE1 B:GLU81 4.6 32.5 1.0
CA B:ASP87 4.8 15.2 1.0
CD B:GLU81 4.9 33.7 1.0
C B:ASP87 4.9 12.4 1.0

Reference:

F.A.Almalki, C.S.Flemming, J.Zhang, M.Feng, S.E.Sedelnikova, T.Ceska, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk. Direct Observation of Dna Threading in Flap Endonuclease Complexes. Nat.Struct.Mol.Biol. V. 23 640 2016.
ISSN: ESSN 1545-9985
PubMed: 27273516
DOI: 10.1038/NSMB.3241
Page generated: Sun Sep 29 16:01:31 2024

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