Magnesium in PDB 8yzu: Stc Truncated Syda

The structure of Stc Truncated Syda, PDB code: 8yzu was solved by A.Fan, S.Fan, M.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.25 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.151, 125, 93.14, 90, 100.65, 90
R / Rfree (%)	18.5 / 23

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Stc Truncated Syda (pdb code 8yzu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Stc Truncated Syda, PDB code: 8yzu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.4 occ:1.00 O A:HOH522 1.9 13.7 1.0 O2 A:POP401 2.0 15.0 1.0 OD1 A:ASP99 2.1 13.4 1.0 O A:HOH507 2.1 11.9 1.0 O A:HOH573 2.2 14.1 1.0 O A:HOH529 2.3 13.9 1.0 CG A:ASP99 3.1 15.6 1.0 MG A:MG403 3.2 13.2 1.0 P1 A:POP401 3.3 14.2 1.0 OD2 A:ASP99 3.4 14.7 1.0 O3 A:POP401 3.4 16.9 1.0 OE2 A:GLU163 4.0 17.6 1.0 O A:HOH540 4.1 17.9 1.0 O1 A:POP401 4.2 14.1 1.0 OE1 A:GLU163 4.2 15.6 1.0 O A:THR185 4.3 13.5 1.0 O A:HOH611 4.3 16.0 1.0 O A:HOH621 4.3 14.0 1.0 O A:HOH553 4.4 12.0 1.0 O A:POP401 4.4 15.2 1.0 CB A:ASP99 4.5 14.4 1.0 CD A:GLU163 4.5 16.1 1.0 CB A:THR185 4.5 15.6 1.0 CE1 A:PHE156 4.6 14.3 1.0 OG1 A:THR160 4.6 15.6 1.0 O A:HOH579 4.8 12.8 1.0 O5 A:POP401 4.9 15.0 1.0

Magnesium binding site 2 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:13.2 occ:1.00 O2 A:POP401 2.0 15.0 1.0 O A:HOH621 2.0 14.0 1.0 O A:HOH529 2.1 13.9 1.0 O A:HOH579 2.1 12.8 1.0 O5 A:POP401 2.1 15.0 1.0 OD2 A:ASP99 2.1 14.7 1.0 P1 A:POP401 3.0 14.2 1.0 CG A:ASP99 3.1 15.6 1.0 MG A:MG402 3.2 15.4 1.0 P2 A:POP401 3.2 14.1 1.0 O A:POP401 3.3 15.2 1.0 OD1 A:ASP99 3.4 13.4 1.0 O1 A:POP401 3.5 14.1 1.0 NZ A:LYS232 3.8 13.8 1.0 NH2 A:ARG304 4.1 14.3 1.0 O4 A:POP401 4.1 16.6 1.0 O A:HOH507 4.2 11.9 1.0 O3 A:POP401 4.3 16.9 1.0 O6 A:POP401 4.3 15.1 1.0 OE2 A:GLU233 4.3 15.1 1.0 O A:HOH540 4.4 17.9 1.0 CB A:ASP99 4.5 14.4 1.0 O A:HOH553 4.5 12.0 1.0 O A:HOH611 4.6 16.0 1.0 O A:HOH522 4.6 13.7 1.0 MG A:MG404 4.6 16.2 1.0 OE1 A:GLU239 4.7 18.4 1.0 OE2 A:GLU100 4.8 28.2 1.0 O A:HOH590 4.8 19.8 1.0 CE A:LYS232 4.9 14.1 1.0

Magnesium binding site 3 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:16.2 occ:1.00 OE2 A:GLU233 2.0 15.1 1.0 O4 A:POP401 2.0 16.6 1.0 O1 A:POP401 2.0 14.1 1.0 O A:HOH565 2.1 14.5 1.0 OD1 A:ASN225 2.2 14.7 1.0 OG A:SER229 2.3 15.1 1.0 CD A:GLU233 3.0 17.7 1.0 P2 A:POP401 3.1 14.1 1.0 P1 A:POP401 3.2 14.2 1.0 CG A:ASN225 3.2 15.6 1.0 CB A:SER229 3.2 15.8 1.0 O A:POP401 3.3 15.2 1.0 OE1 A:GLU233 3.5 17.4 1.0 ND2 A:ASN225 3.6 15.3 1.0 O5 A:POP401 3.8 15.0 1.0 O A:HOH553 3.9 12.0 1.0 O A:ASN225 4.0 15.7 1.0 O A:HOH621 4.1 14.0 1.0 O3 A:POP401 4.2 16.9 1.0 NH2 A:ARG182 4.2 13.0 1.0 O2 A:POP401 4.2 15.0 1.0 CG A:GLU233 4.3 15.6 1.0 O6 A:POP401 4.4 15.1 1.0 C A:ASN225 4.4 15.5 1.0 CB A:ASN225 4.5 15.9 1.0 CA A:SER229 4.6 16.2 1.0 OD1 A:ASP226 4.6 15.4 1.0 MG A:MG403 4.6 13.2 1.0 CE A:LYS232 4.8 14.1 1.0 N A:ASP226 4.8 17.7 1.0 O A:SER229 4.9 17.3 1.0 CA A:ASP226 4.9 16.2 1.0 C A:SER229 4.9 17.3 1.0 CZ A:ARG182 5.0 15.9 1.0

Magnesium binding site 4 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:15.9 occ:1.00 OE2 B:GLU233 2.0 15.9 1.0 O1 B:POP401 2.0 13.6 1.0 OD1 B:ASN225 2.0 13.2 1.0 O4 B:POP401 2.1 16.0 1.0 O B:HOH554 2.2 13.6 1.0 OG B:SER229 2.3 16.1 1.0 CD B:GLU233 3.0 17.4 1.0 CG B:ASN225 3.1 15.7 1.0 P1 B:POP401 3.2 16.6 1.0 P2 B:POP401 3.2 17.3 1.0 CB B:SER229 3.3 15.1 1.0 O B:POP401 3.4 13.9 1.0 OE1 B:GLU233 3.4 17.2 1.0 ND2 B:ASN225 3.6 12.6 1.0 O5 B:POP401 3.8 15.0 1.0 O B:HOH544 3.9 12.9 1.0 O B:HOH567 3.9 13.5 1.0 O B:ASN225 4.0 16.8 1.0 O3 B:POP401 4.1 14.1 1.0 NH2 B:ARG182 4.2 15.5 1.0 O2 B:POP401 4.2 11.4 1.0 CG B:GLU233 4.2 15.9 1.0 C B:ASN225 4.3 15.3 1.0 CB B:ASN225 4.4 14.7 1.0 O6 B:POP401 4.5 14.6 1.0 OD1 B:ASP226 4.6 14.4 1.0 CA B:SER229 4.6 14.7 1.0 N B:ASP226 4.7 15.1 1.0 MG B:MG404 4.8 15.2 1.0 CA B:ASP226 4.8 15.9 1.0 CZ B:ARG182 4.9 14.4 1.0 CE B:LYS232 4.9 15.1 1.0 O B:SER229 5.0 14.6 1.0 NH1 B:ARG182 5.0 14.2 1.0 C B:SER229 5.0 14.7 1.0 O B:HOH570 5.0 13.9 1.0 CA B:ASN225 5.0 16.9 1.0

Magnesium binding site 5 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:15.6 occ:1.00 O B:HOH563 1.9 15.6 1.0 OD1 B:ASP99 2.0 15.5 1.0 O2 B:POP401 2.0 11.4 1.0 O B:HOH607 2.1 14.1 1.0 O B:HOH545 2.2 14.8 1.0 O B:HOH502 2.3 14.6 1.0 CG B:ASP99 3.0 16.3 1.0 MG B:MG404 3.1 15.2 1.0 OD2 B:ASP99 3.3 13.2 1.0 P1 B:POP401 3.3 16.6 1.0 O3 B:POP401 3.6 14.1 1.0 OE1 B:GLU163 4.1 20.3 1.0 O B:HOH560 4.1 16.2 1.0 O1 B:POP401 4.2 13.6 1.0 O B:HOH544 4.2 12.9 1.0 O B:HOH567 4.3 13.5 1.0 O B:HOH586 4.3 15.6 1.0 O B:POP401 4.4 13.9 1.0 CB B:ASP99 4.4 17.2 1.0 OE2 B:GLU163 4.4 18.7 1.0 O B:THR185 4.5 14.6 1.0 CD B:GLU163 4.6 18.9 1.0 OG1 B:THR160 4.6 15.3 1.0 O5 B:POP401 4.7 15.0 1.0 CB B:THR185 4.7 14.8 1.0 CE1 B:PHE156 4.7 14.8 1.0 O B:HOH619 4.8 13.9 1.0

Magnesium binding site 6 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:15.2 occ:1.00 O B:HOH567 2.0 13.5 1.0 O5 B:POP401 2.0 15.0 1.0 O B:HOH545 2.1 14.8 1.0 O B:HOH619 2.1 13.9 1.0 O2 B:POP401 2.1 11.4 1.0 OD2 B:ASP99 2.2 13.2 1.0 MG B:MG403 3.1 15.6 1.0 CG B:ASP99 3.1 16.3 1.0 P1 B:POP401 3.2 16.6 1.0 P2 B:POP401 3.3 17.3 1.0 OD1 B:ASP99 3.4 15.5 1.0 O B:POP401 3.5 13.9 1.0 O1 B:POP401 3.7 13.6 1.0 NZ B:LYS232 3.8 16.4 1.0 NH2 B:ARG304 4.0 17.3 1.0 O4 B:POP401 4.2 16.0 1.0 OE2 B:GLU233 4.3 15.9 1.0 O6 B:POP401 4.3 14.6 1.0 O B:HOH502 4.4 14.6 1.0 O B:HOH560 4.4 16.2 1.0 OE1 B:GLU100 4.5 23.3 1.0 O3 B:POP401 4.5 14.1 1.0 O B:HOH563 4.5 15.6 1.0 O B:HOH544 4.5 12.9 1.0 OE1 B:GLU239 4.5 19.0 1.0 CB B:ASP99 4.5 17.2 1.0 O B:HOH586 4.6 15.6 1.0 O B:HOH731 4.7 22.2 1.0 MG B:MG402 4.8 15.9 1.0 O B:HOH580 4.9 17.6 1.0 O B:HOH607 4.9 14.1 1.0 CE B:LYS232 5.0 15.1 1.0

Magnesium binding site 7 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:21.6 occ:1.00 O5 C:POP401 2.0 24.7 1.0 OE2 C:GLU233 2.1 25.2 1.0 O C:HOH549 2.2 22.8 1.0 OD1 C:ASN225 2.2 24.6 1.0 OG C:SER229 2.2 24.4 1.0 O2 C:POP401 2.3 25.4 1.0 CG C:ASN225 3.1 23.9 1.0 CD C:GLU233 3.1 25.3 1.0 CB C:SER229 3.1 24.6 1.0 P2 C:POP401 3.2 20.9 1.0 ND2 C:ASN225 3.3 24.2 1.0 P1 C:POP401 3.4 22.5 1.0 O C:POP401 3.4 20.0 1.0 OE1 C:GLU233 3.5 25.1 1.0 O4 C:POP401 3.9 22.4 1.0 O C:ASN225 4.0 23.9 1.0 O C:HOH522 4.0 23.6 1.0 NH2 C:ARG182 4.2 30.9 1.0 CG C:GLU233 4.3 26.1 1.0 O C:HOH519 4.3 22.1 1.0 O3 C:POP401 4.3 20.1 1.0 C C:ASN225 4.3 23.7 1.0 O6 C:POP401 4.4 18.3 1.0 CB C:ASN225 4.4 23.6 1.0 O1 C:POP401 4.4 25.6 1.0 CA C:SER229 4.5 24.7 1.0 N C:ASP226 4.8 24.5 1.0 OD2 C:ASP226 4.8 25.5 1.0 MG C:MG403 4.8 23.6 1.0 C C:SER229 4.8 24.8 1.0 CA C:ASP226 4.9 24.9 1.0 O C:SER229 4.9 25.1 1.0 CE C:LYS232 4.9 27.6 1.0 CZ C:ARG182 5.0 29.7 1.0 NH1 C:ARG182 5.0 29.3 1.0 CA C:ASN225 5.0 23.6 1.0

Magnesium binding site 8 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:23.6 occ:1.00 O1 C:POP401 2.0 25.6 1.0 O4 C:POP401 2.1 22.4 1.0 O C:HOH519 2.2 22.1 1.0 OD2 C:ASP99 2.2 26.0 1.0 O C:HOH586 2.2 23.4 1.0 O C:HOH606 2.4 26.3 1.0 P1 C:POP401 3.1 22.5 1.0 CG C:ASP99 3.1 26.8 1.0 P2 C:POP401 3.3 20.9 1.0 OD1 C:ASP99 3.3 25.7 1.0 O C:HOH662 3.3 30.8 1.0 MG C:MG404 3.4 27.5 1.0 O C:POP401 3.4 20.0 1.0 O2 C:POP401 3.5 25.4 1.0 NZ C:LYS232 3.9 25.9 1.0 O C:HOH507 4.0 23.2 1.0 O5 C:POP401 4.2 24.7 1.0 NH2 C:ARG304 4.2 25.8 1.0 OE2 C:GLU233 4.3 25.2 1.0 O C:HOH594 4.3 27.8 1.0 O C:HOH540 4.4 31.0 1.0 O C:HOH522 4.4 23.6 1.0 O3 C:POP401 4.4 20.1 1.0 O6 C:POP401 4.4 18.3 1.0 O C:HOH532 4.5 26.6 1.0 OE1 C:GLU239 4.5 30.9 1.0 CB C:ASP99 4.5 27.3 1.0 O C:HOH570 4.5 30.0 1.0 O C:HOH516 4.6 24.4 1.0 MG C:MG402 4.8 21.6 1.0 O C:HOH550 4.9 24.3 1.0

Magnesium binding site 9 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:27.5 occ:1.00 O C:HOH516 1.9 24.4 1.0 O C:HOH507 2.0 23.2 1.0 O C:HOH550 2.1 24.3 1.0 O1 C:POP401 2.1 25.6 1.0 OD1 C:ASP99 2.2 25.7 1.0 O C:HOH586 2.7 23.4 1.0 CG C:ASP99 3.2 26.8 1.0 P1 C:POP401 3.3 22.5 1.0 O3 C:POP401 3.4 20.1 1.0 MG C:MG403 3.4 23.6 1.0 OD2 C:ASP99 3.6 26.0 1.0 OE1 C:GLU163 3.9 29.3 1.0 O C:THR185 4.1 28.7 1.0 O2 C:POP401 4.2 25.4 1.0 OE2 C:GLU163 4.2 26.2 1.0 CE1 C:PHE156 4.3 28.6 1.0 O C:HOH594 4.4 27.8 1.0 O C:POP401 4.4 20.0 1.0 O C:HOH522 4.4 23.6 1.0 CB C:THR185 4.5 27.9 1.0 CD C:GLU163 4.5 30.7 1.0 O C:HOH532 4.5 26.6 1.0 CB C:ASP99 4.5 27.3 1.0 OG1 C:THR160 4.5 27.3 1.0 O C:HOH519 4.7 22.1 1.0 C C:THR185 4.9 28.0 1.0 NH1 C:ARG182 4.9 29.3 1.0 O4 C:POP401 4.9 22.4 1.0

Magnesium binding site 10 out of 12 in the Stc Truncated Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Stc Truncated Syda within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:25.2 occ:1.00 OD1 D:ASN225 1.9 26.8 1.0 O3 D:POP401 2.1 25.2 1.0 O6 D:POP401 2.1 25.5 1.0 OE2 D:GLU233 2.2 27.2 1.0 O D:HOH510 2.2 23.2 1.0 OG D:SER229 2.4 26.9 1.0 CG D:ASN225 3.0 27.5 1.0 CD D:GLU233 3.1 27.6 1.0 P2 D:POP401 3.2 26.2 1.0 P1 D:POP401 3.2 24.2 1.0 O D:POP401 3.2 21.1 1.0 ND2 D:ASN225 3.4 27.1 1.0 OE1 D:GLU233 3.4 27.2 1.0 CB D:SER229 3.5 27.2 1.0 O D:ASN225 3.9 27.4 1.0 O5 D:POP401 3.9 18.7 1.0 NH2 D:ARG182 4.0 31.0 1.0 O1 D:POP401 4.1 22.5 1.0 O D:HOH575 4.2 20.1 1.0 C D:ASN225 4.2 26.8 1.0 O2 D:POP401 4.3 18.9 1.0 CB D:ASN225 4.3 26.7 1.0 CG D:GLU233 4.3 29.3 1.0 O D:HOH529 4.4 25.5 1.0 O4 D:POP401 4.4 20.7 1.0 OD1 D:ASP226 4.5 29.4 1.0 N D:ASP226 4.6 29.6 1.0 CA D:ASP226 4.7 27.1 1.0 CA D:SER229 4.8 27.4 1.0 CZ D:ARG182 4.8 29.6 1.0 NH1 D:ARG182 4.9 29.2 1.0 CA D:ASN225 4.9 27.6 1.0 MG D:MG404 4.9 23.2 1.0 O D:HOH506 4.9 26.7 1.0

A.Fan, S.Fan, M.Wu. Stc Truncated Syda To Be Published.