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Magnesium in PDB 6ve1: Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH

Enzymatic activity of Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH

All present enzymatic activity of Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH:
3.2.1.96;

Protein crystallography data

The structure of Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH, PDB code: 6ve1 was solved by T.R.Stachowski, M.E.Snell, E.S.Snell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.03 / 2.10
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.480, 99.480, 135.120, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH (pdb code 6ve1). 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 Endo-Beta-N-Acetylglucosaminidase H at High pH, PDB code: 6ve1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6ve1

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Magnesium binding site 1 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:24.9
occ:0.85
 OD2 A:ASP187 1.9 36.3 1.0
O A:HOH522 2.5 12.4 1.0
HB3 A:ALA209 2.7 11.4 1.0
HB2 A:ALA209 2.9 11.4 1.0
O B:ASP239 3.0 15.0 1.0
CG A:ASP187 3.0 28.0 1.0
CB A:ALA209 3.2 9.5 1.0
H A:ALA209 3.5 13.4 1.0
HG A:SER189 3.6 21.4 1.0
OG A:SER189 3.6 17.9 1.0
OD1 A:ASP187 3.6 24.2 1.0
HA B:ASP239 3.7 13.2 1.0
HB1 A:ALA209 3.9 11.4 1.0
O A:HOH637 3.9 38.9 1.0
C B:ASP239 4.0 11.6 1.0
HB2 A:ASP187 4.1 30.4 1.0
CB A:ASP187 4.1 25.4 1.0
N A:ALA209 4.2 11.2 1.0
HB2 A:SER189 4.2 20.5 1.0
CA A:ALA209 4.3 12.8 1.0
HB3 A:ASP187 4.4 30.4 1.0
CA B:ASP239 4.4 11.0 1.0
CB A:SER189 4.4 17.1 1.0
O B:VAL238 4.7 10.0 1.0
O A:HOH553 4.8 24.6 1.0
HB3 A:SER189 4.8 20.5 1.0
HB3 B:ASP239 4.9 15.8 1.0
HB2 A:SER182 4.9 21.6 1.0
HA A:ALA209 4.9 15.4 1.0
HA A:ILE208 5.0 8.4 1.0

Magnesium binding site 2 out of 6 in 6ve1

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Magnesium binding site 2 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:30.6
occ:1.00
 O A:HOH498 2.5 12.4 1.0
O A:ASP190 3.7 16.7 1.0
HE22 A:GLN214 3.8 13.1 1.0
O A:HOH451 3.9 32.6 1.0
O A:PHE192 4.0 11.8 1.0
HA A:ASP193 4.1 10.9 1.0
OD1 A:ASP193 4.5 17.0 1.0
NE2 A:GLN214 4.5 10.9 1.0
C A:ASP190 4.8 14.9 1.0
HE21 A:GLN214 4.8 13.1 1.0
C A:PHE192 4.9 12.3 1.0
O A:HOH515 4.9 20.4 1.0
O A:HOH634 4.9 21.7 1.0
CA A:ASP193 5.0 9.1 1.0
CG A:ASP193 5.0 11.7 1.0

Magnesium binding site 3 out of 6 in 6ve1

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Magnesium binding site 3 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:25.7
occ:1.00
 HE22 B:GLN214 2.2 14.8 1.0
O B:PHE192 2.6 9.1 1.0
HD21 B:LEU210 2.8 15.7 1.0
NE2 B:GLN214 3.0 12.3 1.0
O B:HOH647 3.1 24.0 1.0
O B:ASP190 3.1 14.4 1.0
HD22 B:LEU210 3.3 15.7 1.0
HA B:ASP190 3.3 19.9 1.0
CD2 B:LEU210 3.3 13.1 1.0
O B:HOH401 3.4 25.9 1.0
HE21 B:GLN214 3.4 14.8 1.0
HD23 B:LEU210 3.4 15.7 1.0
HA B:ASP193 3.7 8.9 1.0
C B:ASP190 3.8 15.2 1.0
C B:PHE192 3.8 11.1 1.0
O B:HOH450 3.9 21.9 1.0
CD B:GLN214 4.0 10.6 1.0
CA B:ASP190 4.0 16.6 1.0
OE1 B:GLN214 4.1 17.2 1.0
HB2 B:ASP190 4.2 22.3 1.0
CA B:ASP193 4.5 7.4 1.0
H B:PHE192 4.6 14.2 1.0
O B:SER189 4.6 11.1 1.0
N B:ASP193 4.6 9.1 1.0
CB B:ASP190 4.6 18.6 1.0
N B:PHE192 4.6 11.8 1.0
HD2 B:PRO211 4.7 16.7 1.0
HD11 B:LEU210 4.7 8.2 1.0
CG B:LEU210 4.7 7.7 1.0
N B:LYS191 4.8 16.9 1.0
CA B:PHE192 4.9 10.8 1.0
HD3 B:PRO211 5.0 16.7 1.0
O B:ASP193 5.0 11.5 1.0

Magnesium binding site 4 out of 6 in 6ve1

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Magnesium binding site 4 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:26.7
occ:1.00
 H C:ALA49 2.7 11.4 1.0
HD21 C:ASN22 3.0 25.3 1.0
HD21 C:ASN66 3.1 17.5 1.0
N C:ALA49 3.3 9.5 1.0
O C:HOH464 3.3 14.2 1.0
ND2 C:ASN22 3.4 21.1 1.0
HD22 C:ASN66 3.5 17.5 1.0
ND2 C:ASN66 3.6 14.6 1.0
O C:ALA49 3.7 7.7 1.0
HB3 C:ALA49 3.7 12.4 1.0
O C:PHE48 3.7 8.9 1.0
HD22 C:ASN22 3.8 25.3 1.0
C C:PHE48 3.8 8.2 1.0
HD1 C:PHE48 3.9 9.5 1.0
CG C:ASN22 4.0 17.1 1.0
OD1 C:ASN22 4.1 20.4 1.0
HE1 C:PHE48 4.2 10.6 1.0
CA C:ALA49 4.2 7.4 1.0
CD1 C:PHE48 4.3 7.9 1.0
C C:ALA49 4.4 11.4 1.0
CB C:ALA49 4.4 10.3 1.0
CE1 C:PHE48 4.4 8.8 1.0
OE1 C:GLU20 4.4 18.9 1.0
HG23 C:VAL69 4.6 15.7 1.0
HG21 C:VAL69 4.6 15.7 1.0
O C:HOH414 4.6 9.3 1.0
H C:ASN22 4.8 21.4 1.0
CG C:ASN66 4.9 17.0 1.0
HB2 C:ASN22 4.9 19.7 1.0
CG2 C:VAL69 5.0 13.1 1.0
HB1 C:ALA49 5.0 12.4 1.0
HD22 C:LEU95 5.0 15.0 1.0
HG22 C:VAL21 5.0 14.0 1.0

Magnesium binding site 5 out of 6 in 6ve1

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Magnesium binding site 5 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:27.4
occ:1.00
 HH21 C:ARG273 2.0 38.0 1.0
HH C:TYR32 2.4 30.0 1.0
O C:GLY253 2.4 23.8 1.0
O C:ASP251 2.5 16.3 1.0
HA2 C:GLY252 2.7 18.5 1.0
NH2 C:ARG273 2.8 31.7 1.0
HE C:ARG273 3.0 35.0 1.0
C C:GLY252 3.0 20.8 1.0
OH C:TYR32 3.2 25.0 1.0
CA C:GLY252 3.2 15.4 1.0
HE2 C:TYR32 3.2 25.1 1.0
N C:GLY253 3.3 23.0 1.0
HB3 C:ASN28 3.3 25.1 1.0
HH22 C:ARG273 3.4 38.0 1.0
O C:GLY252 3.4 19.2 1.0
C C:ASP251 3.4 19.6 1.0
C C:GLY253 3.5 30.6 1.0
H C:GLY253 3.5 27.6 1.0
NE C:ARG273 3.6 29.2 1.0
CZ C:ARG273 3.6 32.4 1.0
HD22 C:ASN28 3.7 20.7 1.0
N C:GLY252 3.7 19.2 1.0
ND2 C:ASN28 3.8 17.3 1.0
CE2 C:TYR32 3.9 20.9 1.0
CG C:ASN28 4.0 17.7 1.0
CA C:GLY253 4.0 21.2 1.0
HD11 C:LEU250 4.0 15.9 1.0
CZ C:TYR32 4.0 22.1 1.0
CB C:ASN28 4.1 20.9 1.0
HA3 C:GLY252 4.1 18.5 1.0
HG2 C:ARG255 4.1 22.8 1.0
HD21 C:ASN28 4.1 20.7 1.0
H C:ARG255 4.1 27.2 1.0
OD1 C:ASP251 4.1 23.7 1.0
HG C:LEU250 4.3 11.3 1.0
HB2 C:ARG255 4.4 22.0 1.0
HA C:ASP254 4.5 36.7 1.0
H C:GLY252 4.5 23.0 1.0
HA2 C:GLY253 4.6 25.5 1.0
HD12 C:LEU250 4.6 15.9 1.0
OD1 C:ASN28 4.6 14.6 1.0
HA3 C:GLY253 4.6 25.5 1.0
HD2 C:LYS31 4.6 28.8 1.0
N C:ASP254 4.7 30.5 1.0
CD1 C:LEU250 4.7 13.2 1.0
HB2 C:ASN28 4.7 25.1 1.0
CA C:ASP251 4.8 15.1 1.0
H C:ASP251 4.8 14.5 1.0
HA C:ASN28 4.8 14.8 1.0
CG C:ARG255 4.8 19.0 1.0
N C:ARG255 4.8 22.7 1.0
HG3 C:ARG255 4.9 22.8 1.0
NH1 C:ARG273 4.9 32.5 1.0
HD21 C:LEU250 4.9 21.4 1.0
CD C:ARG273 5.0 25.0 1.0
N C:ASP251 5.0 12.1 1.0
CG C:LEU250 5.0 9.4 1.0

Magnesium binding site 6 out of 6 in 6ve1

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Magnesium binding site 6 out of 6 in the Crystal Structure of Endo-Beta-N-Acetylglucosaminidase H at High pH


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 Endo-Beta-N-Acetylglucosaminidase H at High pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:22.9
occ:1.00
 HD22 D:ASN173 2.0 19.4 1.0
HA D:ASN197 2.6 6.1 1.0
HG3 D:PRO206 2.6 11.7 1.0
ND2 D:ASN173 2.9 16.2 1.0
O D:HOH449 2.9 24.1 1.0
HA D:PRO206 2.9 13.5 1.0
HB3 D:ASN173 3.2 10.6 1.0
HB2 D:ASN197 3.2 9.7 1.0
HD21 D:ASN173 3.3 19.4 1.0
O D:GLN204 3.4 7.8 1.0
HD2 D:PRO198 3.4 10.4 1.0
CA D:ASN197 3.4 5.1 1.0
HD3 D:PRO198 3.4 10.4 1.0
CG D:PRO206 3.4 9.8 1.0
HB3 D:GLN204 3.5 13.4 1.0
CA D:PRO206 3.6 11.3 1.0
HD3 D:PRO206 3.6 11.6 1.0
N D:PRO206 3.6 11.7 1.0
CB D:ASN197 3.7 8.1 1.0
HB3 D:PRO206 3.8 14.4 1.0
CD D:PRO206 3.8 9.6 1.0
CD D:PRO198 3.8 8.6 1.0
CB D:PRO206 3.8 12.0 1.0
CG D:ASN173 3.9 10.6 1.0
CB D:ASN173 3.9 8.9 1.0
N D:ASN197 4.0 8.9 1.0
HB2 D:GLN204 4.0 13.4 1.0
C D:VAL205 4.1 8.9 1.0
C D:GLN204 4.1 15.5 1.0
OD1 D:ASN197 4.1 9.6 1.0
CB D:GLN204 4.2 11.2 1.0
HG2 D:PRO206 4.2 11.7 1.0
HB2 D:ASN173 4.2 10.6 1.0
CG D:ASN197 4.2 7.2 1.0
O D:VAL205 4.3 15.4 1.0
O D:TRP196 4.3 4.9 1.0
H D:ASN197 4.4 10.7 1.0
C D:TRP196 4.4 4.5 1.0
C D:ASN197 4.5 5.8 1.0
HB3 D:ASN197 4.6 9.7 1.0
O D:HOH472 4.6 13.2 1.0
N D:PRO198 4.6 7.5 1.0
O D:ASN173 4.6 9.6 1.0
O D:HOH494 4.7 39.1 1.0
HD2 D:TYR199 4.7 9.8 1.0
HD2 D:PRO206 4.7 11.6 1.0
HB2 D:PRO206 4.8 14.4 1.0
CA D:GLN204 4.9 11.0 1.0
N D:VAL205 4.9 14.4 1.0
H D:GLY207 4.9 19.3 1.0
HE2 D:TYR199 5.0 14.4 1.0
C D:PRO206 5.0 9.7 1.0
CA D:VAL205 5.0 9.2 1.0

Reference:

T.R.Stachowski, M.E.Snell, E.H.Snell. Saxs Studies of X-Ray Induced Disulfide Bond Damage: Engineering High-Resolution Insight From A Low-Resolution Technique. Plos One V. 15 39702 2020.
ISSN: ESSN 1932-6203
PubMed: 33201877
DOI: 10.1371/JOURNAL.PONE.0239702
Page generated: Tue Oct 1 22:01:15 2024

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